Aaron Lun
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/csaw |
| Branch: RELEASE_3_7 |
| Last Commit: 6ea86c7 |
| Last Changed Date: 2018-05-31 19:24:04 -0400 (Thu, 31 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:53:48 -0400 (Wed, 17 Oct 2018).
| Package 327/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| csaw 1.14.1 Aaron Lun
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: csaw |
| Version: 1.14.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:csaw.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings csaw_1.14.1.tar.gz |
| StartedAt: 2018-10-16 20:45:08 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:50:09 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 301.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: csaw.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:csaw.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings csaw_1.14.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/csaw.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘csaw/DESCRIPTION’ ... OK
* this is package ‘csaw’ version ‘1.14.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘csaw’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/csaw/libs/csaw.so’:
Found ‘___assert_rtn’, possibly from ‘assert’ (C)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_exit’, possibly from ‘exit’ (C)
Found ‘_printf’, possibly from ‘printf’ (C)
Found ‘_putchar’, possibly from ‘putchar’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘_srand48’, possibly from ‘srand48’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
detailRanges 16.743 0.599 17.496
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-basic.R’
Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ...21d20
< [W::bgzf_read_block] EOF marker is absent. The input is probably truncated
46,50c45,49
< [1] chrA 1-50 *
< [2] chrA 51-100 *
< [3] chrA 101-150 *
< [4] chrA 151-200 *
< [5] chrA 201-250 *
---
> [1] chrA [ 1, 50] *
> [2] chrA [ 51, 100] *
> [3] chrA [101, 150] *
> [4] chrA [151, 200] *
> [5] chrA [201, 250] *
52,56c51,55
< [67] chrC 1101-1150 *
< [68] chrC 1151-1200 *
< [69] chrC 1201-1250 *
< [70] chrC 1251-1300 *
< [71] chrC 1301-1345 *
---
> [67] chrC [1101, 1150] *
> [68] chrC [1151, 1200] *
> [69] chrC [1201, 1250] *
> [70] chrC [1251, 1300] *
> [71] chrC [1301, 1345] *
75,79c74,78
< [1] chrA 1-500 *
< [2] chrA 201-700 *
< [3] chrA 401-900 *
< [4] chrA 601-1100 *
< [5] chrA 801-1298 *
---
> [1] chrA [ 1, 500] *
> [2] chrA [201, 700] *
> [3] chrA [401, 900] *
> [4] chrA [601, 1100] *
> [5] chrA [801, 1298] *
81,85c80,84
< [15] chrC 401-900 *
< [16] chrC 601-1100 *
< [17] chrC 801-1300 *
< [18] chrC 1001-1345 *
< [19] chrC 1201-1345 *
---
> [15] chrC [ 401, 900] *
> [16] chrC [ 601, 1100] *
> [17] chrC [ 801, 1300] *
> [18] chrC [1001, 1345] *
> [19] chrC [1201, 1345] *
120,125c119,124
< [1] chrA 1-100 *
< [2] chrA 51-150 *
< [3] chrA 101-200 *
< [4] chrA 151-200 *
< [5] chrB 1-100 *
< [6] chrB 51-100 *
---
> [1] chrA [ 1, 100] *
> [2] chrA [ 51, 150] *
> [3] chrA [101, 200] *
> [4] chrA [151, 200] *
> [5] chrB [ 1, 100] *
> [6] chrB [ 51, 100] *
142,146c141,145
< [1] chrA 1-100 *
< [2] chrA 51-150 *
< [3] chrA 101-200 *
< [4] chrB 1-100 *
< [5] chrB 51-100 *
---
> [1] chrA [ 1, 100] *
> [2] chrA [ 51, 150] *
> [3] chrA [101, 200] *
> [4] chrB [ 1, 100] *
> [5] chrB [ 51, 100] *
164,169c163,168
< [1] chrA 1-100 *
< [2] chrA 51-150 *
< [3] chrA 101-200 *
< [4] chrA 151-200 *
< [5] chrB 1-100 *
< [6] chrB 51-100 *
---
> [1] chrA [ 1, 100] *
> [2] chrA [ 51, 150] *
> [3] chrA [101, 200] *
> [4] chrA [151, 200] *
> [5] chrB [ 1, 100] *
> [6] chrB [ 51, 100] *
333,337c332,336
< [1] chrA 1-50 *
< [2] chrA 51-100 *
< [3] chrA 101-150 *
< [4] chrA 151-200 *
< [5] chrA 201-250 *
---
> [1] chrA [ 1, 50] *
> [2] chrA [ 51, 100] *
> [3] chrA [101, 150] *
> [4] chrA [151, 200] *
> [5] chrA [201, 250] *
339,343c338,342
< [67] chrC 1101-1150 *
< [68] chrC 1151-1200 *
< [69] chrC 1201-1250 *
< [70] chrC 1251-1300 *
< [71] chrC 1301-1345 *
---
> [67] chrC [1101, 1150] *
> [68] chrC [1151, 1200] *
> [69] chrC [1201, 1250] *
> [70] chrC [1251, 1300] *
> [71] chrC [1301, 1345] *
356,358c355,357
< [1] chrA 1-1298 *
< [2] chrB 1-870 *
< [3] chrC 1-1345 *
---
> [1] chrA [1, 1298] *
> [2] chrB [1, 870] *
> [3] chrC [1, 1345] *
371,378c370,377
< [1] chrA 1-450 *
< [2] chrA 451-850 *
< [3] chrA 851-1298 *
< [4] chrB 1-450 *
< [5] chrB 451-870 *
< [6] chrC 1-450 *
< [7] chrC 451-900 *
< [8] chrC 901-1345 *
---
> [1] chrA [ 1, 450] *
> [2] chrA [451, 850] *
> [3] chrA [851, 1298] *
> [4] chrB [ 1, 450] *
> [5] chrB [451, 870] *
> [6] chrC [ 1, 450] *
> [7] chrC [451, 900] *
> [8] chrC [901, 1345] *
393,397c392,396
< [1] chrA 1-50 *
< [2] chrA 51-150 *
< [3] chrA 151-200 *
< [4] chrA 201-350 *
< [5] chrA 351-450 *
---
> [1] chrA [ 1, 50] *
> [2] chrA [ 51, 150] *
> [3] chrA [151, 200] *
> [4] chrA [201, 350] *
> [5] chrA [351, 450] *
399,403c398,402
< [39] chrC 1051-1100 *
< [40] chrC 1101-1150 *
< [41] chrC 1151-1250 *
< [42] chrC 1251-1300 *
< [43] chrC 1301-1345 *
---
> [39] chrC [1051, 1100] *
> [40] chrC [1101, 1150] *
> [41] chrC [1151, 1250] *
> [42] chrC [1251, 1300] *
> [43] chrC [1301, 1345] *
472,476c471,475
< [1] chrA 94-103 +
< [2] chrA 106-115 +
< [3] chrA 120-129 +
< [4] chrA 120-129 +
< [5] chrA 129-138 +
---
> [1] chrA [ 94, 103] +
> [2] chrA [106, 115] +
> [3] chrA [120, 129] +
> [4] chrA [120, 129] +
> [5] chrA [129, 138] +
478,482c477,481
< [139] chrA 467-476 -
< [140] chrA 482-491 -
< [141] chrA 490-499 -
< [142] chrA 491-500 -
< [143] chrA 499-508 -
---
> [139] chrA [467, 476] -
> [140] chrA [482, 491] -
> [141] chrA [490, 499] -
> [142] chrA [491, 500] -
> [143] chrA [499, 508] -
489,493c488,492
< [1] chrA 43-52 +
< [2] chrA 51-60 +
< [3] chrA 57-66 +
< [4] chrA 62-71 +
< [5] chrA 63-72 +
---
> [1] chrA [43, 52] +
> [2] chrA [51, 60] +
> [3] chrA [57, 66] +
> [4] chrA [62, 71] +
> [5] chrA [63, 72] +
495,499c494,498
< [23] chrA 79-88 -
< [24] chrA 83-92 -
< [25] chrA 88-97 -
< [26] chrA 89-98 -
< [27] chrA 93-102 -
---
> [23] chrA [79, 88] -
> [24] chrA [83, 92] -
> [25] chrA [88, 97] -
> [26] chrA [89, 98] -
> [27] chrA [93, 102] -
506,510c505,509
< [1] chrA 51-60 +
< [2] chrA 57-66 +
< [3] chrA 62-71 +
< [4] chrA 63-72 +
< [5] chrA 76-85 +
---
> [1] chrA [51, 60] +
> [2] chrA [57, 66] +
> [3] chrA [62, 71] +
> [4] chrA [63, 72] +
> [5] chrA [76, 85] +
512,516c511,515
< [15] chrA 79-88 -
< [16] chrA 79-88 -
< [17] chrA 88-97 -
< [18] chrA 89-98 -
< [19] chrA 93-102 -
---
> [15] chrA [79, 88] -
> [16] chrA [79, 88] -
> [17] chrA [88, 97] -
> [18] chrA [89, 98] -
> [19] chrA [93, 102] -
523,525c522,524
< [1] chrB 50-79 *
< [2] chrB 90-99 *
< [3] chrB 99-100 *
---
> [1] chrB [50, 79] *
> [2] chrB [90, 99] *
> [3] chrB [99, 100] *
532,535c531,534
< [1] chrB 75-84 +
< [2] chrB 90-99 +
< [3] chrB 70-79 -
< [4] chrB 99-100 -
---
> [1] chrB [75, 84] +
> [2] chrB [90, 99] +
> [3] chrB [70, 79] -
> [4] chrB [99, 100] -
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/csaw.Rcheck/00check.log’
for details.
csaw.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL csaw ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘csaw’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c annotator.cpp -o annotator.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c bam_utils.cpp -o bam_utils.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c best_in_cluster.cpp -o best_in_cluster.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c check_bimodality.cpp -o check_bimodality.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c correlate_reads.cpp -o correlate_reads.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c find_maxima.cpp -o find_maxima.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c get_cluster_stats.cpp -o get_cluster_stats.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c get_profile.cpp -o get_profile.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c get_rle_counts.cpp -o get_rle_counts.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c merge_windows.cpp -o merge_windows.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c pair_reads.cpp -o pair_reads.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c single_reads.cpp -o single_reads.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o csaw.so annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.o utils.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/csaw/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘csaw.Rnw’ ** testing if installed package can be loaded * DONE (csaw)
csaw.Rcheck/tests/test-basic.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This is a testing stub that just provides a basic run-through of all the methods.
> # The real tests are located in inst/tests along with a Bash script for execution
> # and comparison. The separation into two folders is necessary to keep R CMD check
> # running with reasonable speed.
>
> suppressWarnings(suppressPackageStartupMessages(require(csaw)))
> both.files <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
> pe.file <- system.file("exdata", "pet.bam", package="csaw")
>
> # Checking data quality prior to counting.
> head(correlateReads(both.files))
[1] -0.0137654663 0.0005571408 0.0175021237 -0.0308470292 -0.0087488234
[6] -0.0120687468
> head(correlateReads(both.files, cross=FALSE))
[1] 1.0000000000 -0.0008601215 0.0170688852 -0.0475443596 0.0028128511
[6] -0.0030687197
>
> getPESizes(pe.file)
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
$sizes
[1] 70 90 20 150 10 30 10 2
$diagnostics
total.reads mapped.reads single mate.unmapped unoriented
23 23 3 0 1
inter.chr
1
>
> # Trying to count some single-end data.
> data <- windowCounts(both.files, ext=100)
> head(assay(data))
[,1] [,2]
[1,] 43 71
[2,] 57 89
[3,] 56 120
[4,] 53 141
[5,] 40 152
[6,] 59 135
> rowRanges(data)
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 1-50 *
[2] chrA 51-100 *
[3] chrA 101-150 *
[4] chrA 151-200 *
[5] chrA 201-250 *
... ... ... ...
[67] chrC 1101-1150 *
[68] chrC 1151-1200 *
[69] chrC 1201-1250 *
[70] chrC 1251-1300 *
[71] chrC 1301-1345 *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, width=500, spacing=200)
> head(assay(data))
[,1] [,2]
[1,] 204 455
[2,] 195 510
[3,] 186 483
[4,] 200 501
[5,] 187 468
[6,] 127 311
> rowRanges(data)
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 1-500 *
[2] chrA 201-700 *
[3] chrA 401-900 *
[4] chrA 601-1100 *
[5] chrA 801-1298 *
... ... ... ...
[15] chrC 401-900 *
[16] chrC 601-1100 *
[17] chrC 801-1300 *
[18] chrC 1001-1345 *
[19] chrC 1201-1345 *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100))
> data$totals
[1] 914 2152
> data <- windowCounts(both.files, ext=100, param=readParam(dedup=TRUE))
> data$totals
[1] 1056 2582
> data <- windowCounts(both.files, ext=100, param=readParam(discard=GRanges("chrA", IRanges(50, 500))))
> data$totals
[1] 1186 2916
> data <- windowCounts(both.files, ext=100, param=readParam(restrict="chrA"))
> data$totals
[1] 451 1093
>
> # Trying to count some paired-end data.
> out <- windowCounts(pe.file, param=readParam(pe="both"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 2
[4,] 1
[5,] 4
[6,] 3
> out$totals
[1] 8
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 1-100 *
[2] chrA 51-150 *
[3] chrA 101-200 *
[4] chrA 151-200 *
[5] chrB 1-100 *
[6] chrB 51-100 *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="both", max.frag=100), width=100, filter=1L)
> assay(out)
[,1]
[1,] 2
[2,] 3
[3,] 1
[4,] 4
[5,] 3
> out$totals
[1] 7
> rowRanges(out)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 1-100 *
[2] chrA 51-150 *
[3] chrA 101-200 *
[4] chrB 1-100 *
[5] chrB 51-100 *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="first"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 4
[4,] 2
[5,] 6
[6,] 6
> out$totals
[1] 10
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 1-100 *
[2] chrA 51-150 *
[3] chrA 101-200 *
[4] chrA 151-200 *
[5] chrB 1-100 *
[6] chrB 51-100 *
-------
seqinfo: 2 sequences from an unspecified genome
>
> # Trying to convert it to a DGEList.
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 1
> asDGEList(data, lib.size=c(10, 10))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 10 1
Sample2 1 10 1
> asDGEList(data, norm=c(1,2))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 2
>
> temp <- data
> temp$totals <- NULL
> asDGEList(temp) # Should spit out a warning.
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 1293 1
Sample2 1 3142 1
Warning message:
In .local(object, ...) :
library sizes not found in 'totals', setting to NULL
>
> # Running some basic normalization.
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100, dedup=TRUE))
>
> normOffsets(assay(data), lib.size=data$totals)
[1] 1.001197 0.998804
> normOffsets(assay(data), lib.size=data$totals, logratioTrim=.2)
[1] 1.003816 0.996199
> normOffsets(assay(data), lib.size=data$totals, method="RLE")
[1] 1.0037890 0.9962253
> normOffsets(data)
class: RangedSummarizedExperiment
dim: 71 2
metadata(6): spacing width ... param final.ext
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(5): bam.files totals ext rlen norm.factors
> normOffsets(data, logratioTrim=0.1)
class: RangedSummarizedExperiment
dim: 71 2
metadata(6): spacing width ... param final.ext
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(5): bam.files totals ext rlen norm.factors
> normOffsets(data, method="upperquartile")
class: RangedSummarizedExperiment
dim: 71 2
metadata(6): spacing width ... param final.ext
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(5): bam.files totals ext rlen norm.factors
>
> head(normOffsets(assay(data), lib.size=data$totals, type="loess"))
[,1] [,2]
[1,] -0.4047876 0.4047876
[2,] -0.4328410 0.4328410
[3,] -0.3864553 0.3864553
[4,] -0.4101296 0.4101296
[5,] -0.3788945 0.3788945
[6,] -0.3514597 0.3514597
> head(normOffsets(assay(data), lib.size=data$totals, type="loess", span=0.7))
[,1] [,2]
[1,] -0.4297765 0.4297765
[2,] -0.4391936 0.4391936
[3,] -0.3867962 0.3867962
[4,] -0.4215479 0.4215479
[5,] -0.3858107 0.3858107
[6,] -0.3915074 0.3915074
> head(normOffsets(data, type="loess"))
class: RangedSummarizedExperiment
dim: 6 2
metadata(6): spacing width ... param final.ext
assays(2): counts offset
rownames: NULL
rowData names(0):
colnames: NULL
colData names(4): bam.files totals ext rlen
> head(normOffsets(data, type="loess", span=0.5))
class: RangedSummarizedExperiment
dim: 6 2
metadata(6): spacing width ... param final.ext
assays(2): counts offset
rownames: NULL
rowData names(0):
colnames: NULL
colData names(4): bam.files totals ext rlen
>
> # Assuming someone went around and pulled out some p-values for everybody.
> set.seed(128145-19238)
> nr <- nrow(data)
> tabled <- data.frame(logFC=rnorm(nr), logCPM=rnorm(nr), PValue=rbeta(nr, 1, 2))
> weighting <- rgamma(nr, 2, 1)
>
> mergeWindows(rowRanges(data), -1)
$id
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
[51] 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
$region
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 1-50 *
[2] chrA 51-100 *
[3] chrA 101-150 *
[4] chrA 151-200 *
[5] chrA 201-250 *
... ... ... ...
[67] chrC 1101-1150 *
[68] chrC 1151-1200 *
[69] chrC 1201-1250 *
[70] chrC 1251-1300 *
[71] chrC 1301-1345 *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100)
$id
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2
[39] 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
$region
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 1-1298 *
[2] chrB 1-870 *
[3] chrC 1-1345 *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100, max.width=500)
$id
[1] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 5 5 5
[39] 5 5 5 5 5 5 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8 8 8
$region
GRanges object with 8 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 1-450 *
[2] chrA 451-850 *
[3] chrA 851-1298 *
[4] chrB 1-450 *
[5] chrB 451-870 *
[6] chrC 1-450 *
[7] chrC 451-900 *
[8] chrC 901-1345 *
-------
seqinfo: 3 sequences from an unspecified genome
> merged <- mergeWindows(rowRanges(data), 100, sign=tabled$logFC > 0)
> merged
$id
[1] 1 2 2 3 4 4 4 5 5 6 7 8 9 9 9 9 10 10 11 12 13 14 15 15 15
[26] 15 16 17 18 18 18 18 18 19 19 20 21 22 23 24 24 25 25 26 27 28 29 29 30 30
[51] 31 31 31 31 32 33 34 34 34 34 35 36 37 37 38 39 40 41 41 42 43
$region
GRanges object with 43 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 1-50 *
[2] chrA 51-150 *
[3] chrA 151-200 *
[4] chrA 201-350 *
[5] chrA 351-450 *
... ... ... ...
[39] chrC 1051-1100 *
[40] chrC 1101-1150 *
[41] chrC 1151-1250 *
[42] chrC 1251-1300 *
[43] chrC 1301-1345 *
-------
seqinfo: 3 sequences from an unspecified genome
>
> head(combineTests(merged$id, tabled))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5047602 up
4 3 0 1 0.08956765 0.4125151 down
5 2 1 0 0.28172663 0.5047602 up
6 1 0 1 0.01949563 0.4125151 down
> head(combineTests(merged$id, tabled, weight=weighting))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5228651 up
4 3 0 1 0.04669873 0.4255938 down
5 2 1 0 0.24536526 0.4795776 up
6 1 0 1 0.01949563 0.3373185 down
>
> head(getBestTest(merged$id, tabled))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 3 -0.24872062 -0.73322697 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5047602
4 5 -0.01753979 1.78172679 0.08956765 0.4442470
5 9 0.21512818 1.42847478 0.28172663 0.5047602
6 10 -1.10068046 -0.09313516 0.01949563 0.4442470
> head(getBestTest(merged$id, tabled, weight=weighting))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 2 -0.41696325 1.60566251 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.04669873 0.4255938
5 9 0.21512818 1.42847478 0.24536526 0.4795776
6 10 -1.10068046 -0.09313516 0.01949563 0.3373185
> head(getBestTest(merged$id, tabled, by.pval=FALSE))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5622769
2 2 -0.41696325 1.60566251 0.79272727 0.8116017
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.02985588 0.2567606
5 9 0.21512818 1.42847478 0.14086332 0.4038082
6 10 -1.10068046 -0.09313516 0.01949563 0.2567606
>
> # Pulling out some diagnostics.
> suppressPackageStartupMessages(require(org.Mm.eg.db))
> suppressPackageStartupMessages(require(TxDb.Mmusculus.UCSC.mm10.knownGene))
>
> current <- readRDS(system.file("exdata", "exrange.rds", package="csaw"))
> output <- detailRanges(current, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db)
> head(output$overlap)
[1] "Nrxn3|8|+" "" ""
[4] "1700007G11Rik|I|+" "Mannr|2|+" ""
> head(output$right)
[1] "Nrxn3|9|+[3846]" "Rprm|1|-[2293]" "" ""
[5] "" ""
> head(output$left)
[1] "" ""
[3] "" "1700007G11Rik|5|+[2890]"
[5] "" ""
>
> # Pulling out some reads.
> extractReads(both.files[1], GRanges("chrA", IRanges(100, 500)))
GRanges object with 143 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 94-103 +
[2] chrA 106-115 +
[3] chrA 120-129 +
[4] chrA 120-129 +
[5] chrA 129-138 +
... ... ... ...
[139] chrA 467-476 -
[140] chrA 482-491 -
[141] chrA 490-499 -
[142] chrA 491-500 -
[143] chrA 499-508 -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)))
GRanges object with 27 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 43-52 +
[2] chrA 51-60 +
[3] chrA 57-66 +
[4] chrA 62-71 +
[5] chrA 63-72 +
... ... ... ...
[23] chrA 79-88 -
[24] chrA 83-92 -
[25] chrA 88-97 -
[26] chrA 89-98 -
[27] chrA 93-102 -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)), param=readParam(dedup=TRUE))
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA 51-60 +
[2] chrA 57-66 +
[3] chrA 62-71 +
[4] chrA 63-72 +
[5] chrA 76-85 +
... ... ... ...
[15] chrA 79-88 -
[16] chrA 79-88 -
[17] chrA 88-97 -
[18] chrA 89-98 -
[19] chrA 93-102 -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="both"))
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB 50-79 *
[2] chrB 90-99 *
[3] chrB 99-100 *
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="second"))
GRanges object with 4 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB 75-84 +
[2] chrB 90-99 +
[3] chrB 70-79 -
[4] chrB 99-100 -
-------
seqinfo: 1 sequence from an unspecified genome
>
>
> proc.time()
user system elapsed
24.467 1.134 25.823
csaw.Rcheck/tests/test-basic.Rout.save
R Under development (unstable) (2017-10-27 r73632) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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> # This is a testing stub that just provides a basic run-through of all the methods.
> # The real tests are located in inst/tests along with a Bash script for execution
> # and comparison. The separation into two folders is necessary to keep R CMD check
> # running with reasonable speed.
>
> suppressWarnings(suppressPackageStartupMessages(require(csaw)))
> both.files <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
> pe.file <- system.file("exdata", "pet.bam", package="csaw")
>
> # Checking data quality prior to counting.
> head(correlateReads(both.files))
[1] -0.0137654663 0.0005571408 0.0175021237 -0.0308470292 -0.0087488234
[6] -0.0120687468
> head(correlateReads(both.files, cross=FALSE))
[1] 1.0000000000 -0.0008601215 0.0170688852 -0.0475443596 0.0028128511
[6] -0.0030687197
>
> getPESizes(pe.file)
$sizes
[1] 70 90 20 150 10 30 10 2
$diagnostics
total.reads mapped.reads single mate.unmapped unoriented
23 23 3 0 1
inter.chr
1
>
> # Trying to count some single-end data.
> data <- windowCounts(both.files, ext=100)
> head(assay(data))
[,1] [,2]
[1,] 43 71
[2,] 57 89
[3,] 56 120
[4,] 53 141
[5,] 40 152
[6,] 59 135
> rowRanges(data)
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 100] *
[3] chrA [101, 150] *
[4] chrA [151, 200] *
[5] chrA [201, 250] *
... ... ... ...
[67] chrC [1101, 1150] *
[68] chrC [1151, 1200] *
[69] chrC [1201, 1250] *
[70] chrC [1251, 1300] *
[71] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, width=500, spacing=200)
> head(assay(data))
[,1] [,2]
[1,] 204 455
[2,] 195 510
[3,] 186 483
[4,] 200 501
[5,] 187 468
[6,] 127 311
> rowRanges(data)
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 500] *
[2] chrA [201, 700] *
[3] chrA [401, 900] *
[4] chrA [601, 1100] *
[5] chrA [801, 1298] *
... ... ... ...
[15] chrC [ 401, 900] *
[16] chrC [ 601, 1100] *
[17] chrC [ 801, 1300] *
[18] chrC [1001, 1345] *
[19] chrC [1201, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100))
> data$totals
[1] 914 2152
> data <- windowCounts(both.files, ext=100, param=readParam(dedup=TRUE))
> data$totals
[1] 1056 2582
> data <- windowCounts(both.files, ext=100, param=readParam(discard=GRanges("chrA", IRanges(50, 500))))
> data$totals
[1] 1186 2916
> data <- windowCounts(both.files, ext=100, param=readParam(restrict="chrA"))
> data$totals
[1] 451 1093
>
> # Trying to count some paired-end data.
> out <- windowCounts(pe.file, param=readParam(pe="both"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 2
[4,] 1
[5,] 4
[6,] 3
> out$totals
[1] 8
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrA [151, 200] *
[5] chrB [ 1, 100] *
[6] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="both", max.frag=100), width=100, filter=1L)
> assay(out)
[,1]
[1,] 2
[2,] 3
[3,] 1
[4,] 4
[5,] 3
> out$totals
[1] 7
> rowRanges(out)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrB [ 1, 100] *
[5] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="first"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 4
[4,] 2
[5,] 6
[6,] 6
> out$totals
[1] 10
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrA [151, 200] *
[5] chrB [ 1, 100] *
[6] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
>
> # Trying to convert it to a DGEList.
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 1
> asDGEList(data, lib.size=c(10, 10))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 10 1
Sample2 1 10 1
> asDGEList(data, norm=c(1,2))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 2
>
> temp <- data
> temp$totals <- NULL
> asDGEList(temp) # Should spit out a warning.
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 1293 1
Sample2 1 3142 1
Warning message:
In .local(object, ...) :
library sizes not found in 'totals', setting to NULL
>
> # Running some basic normalization.
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100, dedup=TRUE))
>
> normOffsets(assay(data), lib.size=data$totals)
[1] 1.001197 0.998804
> normOffsets(assay(data), lib.size=data$totals, logratioTrim=.2)
[1] 1.003816 0.996199
> normOffsets(assay(data), lib.size=data$totals, method="RLE")
[1] 1.0037890 0.9962253
> normOffsets(data)
class: RangedSummarizedExperiment
dim: 71 2
metadata(6): spacing width ... param final.ext
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(5): bam.files totals ext rlen norm.factors
> normOffsets(data, logratioTrim=0.1)
class: RangedSummarizedExperiment
dim: 71 2
metadata(6): spacing width ... param final.ext
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(5): bam.files totals ext rlen norm.factors
> normOffsets(data, method="upperquartile")
class: RangedSummarizedExperiment
dim: 71 2
metadata(6): spacing width ... param final.ext
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(5): bam.files totals ext rlen norm.factors
>
> head(normOffsets(assay(data), lib.size=data$totals, type="loess"))
[,1] [,2]
[1,] -0.4047876 0.4047876
[2,] -0.4328410 0.4328410
[3,] -0.3864553 0.3864553
[4,] -0.4101296 0.4101296
[5,] -0.3788945 0.3788945
[6,] -0.3514597 0.3514597
> head(normOffsets(assay(data), lib.size=data$totals, type="loess", span=0.7))
[,1] [,2]
[1,] -0.4297765 0.4297765
[2,] -0.4391936 0.4391936
[3,] -0.3867962 0.3867962
[4,] -0.4215479 0.4215479
[5,] -0.3858107 0.3858107
[6,] -0.3915074 0.3915074
> head(normOffsets(data, type="loess"))
class: RangedSummarizedExperiment
dim: 6 2
metadata(6): spacing width ... param final.ext
assays(2): counts offset
rownames: NULL
rowData names(0):
colnames: NULL
colData names(4): bam.files totals ext rlen
> head(normOffsets(data, type="loess", span=0.5))
class: RangedSummarizedExperiment
dim: 6 2
metadata(6): spacing width ... param final.ext
assays(2): counts offset
rownames: NULL
rowData names(0):
colnames: NULL
colData names(4): bam.files totals ext rlen
>
> # Assuming someone went around and pulled out some p-values for everybody.
> set.seed(128145-19238)
> nr <- nrow(data)
> tabled <- data.frame(logFC=rnorm(nr), logCPM=rnorm(nr), PValue=rbeta(nr, 1, 2))
> weighting <- rgamma(nr, 2, 1)
>
> mergeWindows(rowRanges(data), -1)
$id
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
[51] 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
$region
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 100] *
[3] chrA [101, 150] *
[4] chrA [151, 200] *
[5] chrA [201, 250] *
... ... ... ...
[67] chrC [1101, 1150] *
[68] chrC [1151, 1200] *
[69] chrC [1201, 1250] *
[70] chrC [1251, 1300] *
[71] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100)
$id
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2
[39] 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
$region
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [1, 1298] *
[2] chrB [1, 870] *
[3] chrC [1, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100, max.width=500)
$id
[1] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 5 5 5
[39] 5 5 5 5 5 5 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8 8 8
$region
GRanges object with 8 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 450] *
[2] chrA [451, 850] *
[3] chrA [851, 1298] *
[4] chrB [ 1, 450] *
[5] chrB [451, 870] *
[6] chrC [ 1, 450] *
[7] chrC [451, 900] *
[8] chrC [901, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> merged <- mergeWindows(rowRanges(data), 100, sign=tabled$logFC > 0)
> merged
$id
[1] 1 2 2 3 4 4 4 5 5 6 7 8 9 9 9 9 10 10 11 12 13 14 15 15 15
[26] 15 16 17 18 18 18 18 18 19 19 20 21 22 23 24 24 25 25 26 27 28 29 29 30 30
[51] 31 31 31 31 32 33 34 34 34 34 35 36 37 37 38 39 40 41 41 42 43
$region
GRanges object with 43 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 150] *
[3] chrA [151, 200] *
[4] chrA [201, 350] *
[5] chrA [351, 450] *
... ... ... ...
[39] chrC [1051, 1100] *
[40] chrC [1101, 1150] *
[41] chrC [1151, 1250] *
[42] chrC [1251, 1300] *
[43] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
>
> head(combineTests(merged$id, tabled))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5047602 up
4 3 0 1 0.08956765 0.4125151 down
5 2 1 0 0.28172663 0.5047602 up
6 1 0 1 0.01949563 0.4125151 down
> head(combineTests(merged$id, tabled, weight=weighting))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5228651 up
4 3 0 1 0.04669873 0.4255938 down
5 2 1 0 0.24536526 0.4795776 up
6 1 0 1 0.01949563 0.3373185 down
>
> head(getBestTest(merged$id, tabled))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 3 -0.24872062 -0.73322697 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5047602
4 5 -0.01753979 1.78172679 0.08956765 0.4442470
5 9 0.21512818 1.42847478 0.28172663 0.5047602
6 10 -1.10068046 -0.09313516 0.01949563 0.4442470
> head(getBestTest(merged$id, tabled, weight=weighting))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 2 -0.41696325 1.60566251 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.04669873 0.4255938
5 9 0.21512818 1.42847478 0.24536526 0.4795776
6 10 -1.10068046 -0.09313516 0.01949563 0.3373185
> head(getBestTest(merged$id, tabled, by.pval=FALSE))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5622769
2 2 -0.41696325 1.60566251 0.79272727 0.8116017
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.02985588 0.2567606
5 9 0.21512818 1.42847478 0.14086332 0.4038082
6 10 -1.10068046 -0.09313516 0.01949563 0.2567606
>
> # Pulling out some diagnostics.
> suppressPackageStartupMessages(require(org.Mm.eg.db))
> suppressPackageStartupMessages(require(TxDb.Mmusculus.UCSC.mm10.knownGene))
>
> current <- readRDS(system.file("exdata", "exrange.rds", package="csaw"))
> output <- detailRanges(current, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db)
> head(output$overlap)
[1] "Nrxn3|8|+" "" ""
[4] "1700007G11Rik|I|+" "Mannr|2|+" ""
> head(output$right)
[1] "Nrxn3|9|+[3846]" "Rprm|1|-[2293]" "" ""
[5] "" ""
> head(output$left)
[1] "" ""
[3] "" "1700007G11Rik|5|+[2890]"
[5] "" ""
>
> # Pulling out some reads.
> extractReads(both.files[1], GRanges("chrA", IRanges(100, 500)))
GRanges object with 143 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 94, 103] +
[2] chrA [106, 115] +
[3] chrA [120, 129] +
[4] chrA [120, 129] +
[5] chrA [129, 138] +
... ... ... ...
[139] chrA [467, 476] -
[140] chrA [482, 491] -
[141] chrA [490, 499] -
[142] chrA [491, 500] -
[143] chrA [499, 508] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)))
GRanges object with 27 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [43, 52] +
[2] chrA [51, 60] +
[3] chrA [57, 66] +
[4] chrA [62, 71] +
[5] chrA [63, 72] +
... ... ... ...
[23] chrA [79, 88] -
[24] chrA [83, 92] -
[25] chrA [88, 97] -
[26] chrA [89, 98] -
[27] chrA [93, 102] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)), param=readParam(dedup=TRUE))
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [51, 60] +
[2] chrA [57, 66] +
[3] chrA [62, 71] +
[4] chrA [63, 72] +
[5] chrA [76, 85] +
... ... ... ...
[15] chrA [79, 88] -
[16] chrA [79, 88] -
[17] chrA [88, 97] -
[18] chrA [89, 98] -
[19] chrA [93, 102] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="both"))
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB [50, 79] *
[2] chrB [90, 99] *
[3] chrB [99, 100] *
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="second"))
GRanges object with 4 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB [75, 84] +
[2] chrB [90, 99] +
[3] chrB [70, 79] -
[4] chrB [99, 100] -
-------
seqinfo: 1 sequence from an unspecified genome
>
>
> proc.time()
user system elapsed
14.644 0.204 14.849
csaw.Rcheck/csaw-Ex.timings
| name | user | system | elapsed | |
| SEmethods | 0.559 | 0.041 | 0.607 | |
| checkBimodality | 0.401 | 0.057 | 0.463 | |
| clusterFDR | 1.010 | 0.087 | 1.105 | |
| clusterWindows | 2.091 | 0.011 | 2.125 | |
| combineTests | 0.023 | 0.001 | 0.024 | |
| consolidateClusters | 3.196 | 0.009 | 3.243 | |
| consolidateSizes | 0.898 | 0.009 | 0.914 | |
| correlateReads | 0.218 | 0.003 | 0.222 | |
| csawUsersGuide | 0.003 | 0.000 | 0.003 | |
| detailRanges | 16.743 | 0.599 | 17.496 | |
| empiricalFDR | 0.008 | 0.000 | 0.008 | |
| extractReads | 1.574 | 0.025 | 1.611 | |
| filterWindows | 0.806 | 0.042 | 0.857 | |
| findMaxima | 0.190 | 0.010 | 0.202 | |
| getBestTest | 0.027 | 0.002 | 0.029 | |
| getPESizes | 0.161 | 0.002 | 0.162 | |
| getWidths | 0.600 | 0.006 | 0.616 | |
| maximizeCcf | 0.004 | 0.000 | 0.004 | |
| mergeWindows | 0.058 | 0.001 | 0.059 | |
| mixedClusters | 0.01 | 0.00 | 0.01 | |
| normOffsets | 0.408 | 0.004 | 0.414 | |
| overlapStats | 0.240 | 0.003 | 0.247 | |
| profileSites | 0.612 | 0.007 | 0.630 | |
| readParam | 0.048 | 0.001 | 0.050 | |
| regionCounts | 0.360 | 0.004 | 0.370 | |
| scaledAverage | 0.597 | 0.004 | 0.608 | |
| strandedCounts | 1.938 | 0.015 | 1.974 | |
| upweightSummit | 0.006 | 0.000 | 0.007 | |
| windowCounts | 1.073 | 0.008 | 1.089 | |
| wwhm | 0.112 | 0.001 | 0.114 | |