Ted Wong
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Anaquin |
| Branch: RELEASE_3_8 |
| Last Commit: 22b6c71 |
| Last Changed Date: 2019-01-04 13:18:49 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:52 -0400 (Tue, 16 Apr 2019).
| Package 48/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Anaquin 2.6.1 Ted Wong
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Anaquin |
| Version: 2.6.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Anaquin.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Anaquin_2.6.1.tar.gz |
| StartedAt: 2019-04-15 22:19:45 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:20:46 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 60.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Anaquin.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Anaquin.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Anaquin_2.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Anaquin.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Anaquin/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Anaquin’ version ‘2.6.1’ * 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 ‘Anaquin’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘ggplot2’ A package should be listed in only one of these fields. * 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 ... NOTE Namespace in Imports field not imported from: ‘DESeq2’ All declared Imports should be used. * 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 ... NOTE prepare_Rd: plotConjoint.Rd:26-27: Dropping empty section \examples * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tPlotLOD.R’ Running ‘tPlotLinear.R’ Running ‘tPlotLogistic.R’ Running ‘tPlotROC.R’ 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.8-bioc/meat/Anaquin.Rcheck/00check.log’ for details.
Anaquin.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Anaquin ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘Anaquin’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Anaquin)
Anaquin.Rcheck/tests/tPlotLinear.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> #
> # Copyright (C) 2016 - Garvan Institute of Medical Research
> #
> # Ted Wong, Bioinformatic Software Engineer at Garvan Institute
> #
>
> library(RUnit)
> library(Anaquin)
Loading required package: ggplot2
>
> .test.data <- function()
+ {
+ input <- c(15.1062,
+ 15.1062,
+ 966.797,
+ 241.699,
+ 30.2124,
+ 7734.38,
+ 483.398,
+ 30937.5,
+ 483.398,
+ 15.1062,
+ 483.398,
+ 241.699,
+ 60.4248,
+ 0.118017,
+ 7734.37,
+ 7734.38,
+ 120.85,
+ 1933.59,
+ 0.944138,
+ 120.85,
+ 7.5531,
+ 3.77655,
+ 3867.19,
+ 15468.8,
+ 1.88828,
+ 1933.59,
+ 120.85,
+ 3867.19,
+ 30.2124,
+ 0.472069,
+ 241.699,
+ 60.4248,
+ 0.944138,
+ 120.85,
+ 1.88828,
+ 60.4248,
+ 15468.8,
+ 60.4248,
+ 1933.59,
+ 1.88828,
+ 30.2124,
+ 0.944138,
+ 3867.19,
+ 15468.8,
+ 3867.19,
+ 30.2124,
+ 15.1062,
+ 1933.59,
+ 7.5531,
+ 0.472069,
+ 0.472069,
+ 0.236034,
+ 0.0590086,
+ 241.699,
+ 0.236034,
+ 0.472069,
+ 0.118017,
+ 120.85,
+ 0.118017,
+ 483.398,
+ 30937.5,
+ 7.5531,
+ 0.472069,
+ 483.398,
+ 7.5531,
+ 966.797,
+ 3.77655,
+ 30937.5,
+ 3.77655,
+ 3.77655,
+ 966.797,
+ 3.77655,
+ 0.236034,
+ 1.88828,
+ 0.0590086)
+
+ o1 <- c(4.29354,
+ 6.41774,
+ 271.696,
+ 67.3212,
+ 3.1943,
+ 2628.81,
+ 245.034,
+ 14727.4,
+ 38.2906,
+ 8.41748,
+ 140.367,
+ 90.1342,
+ 5.03172,
+ 0.282232,
+ 2340.3,
+ 5418.16,
+ 124.648,
+ 157.443,
+ 0.437077,
+ 2.42797,
+ 3.88121,
+ NA,
+ 2010.24,
+ 7762.18,
+ 2.05478,
+ 526.579,
+ 29.9481,
+ 1369.19,
+ 9.21093,
+ 0.305795,
+ 50.4639,
+ 11.4579,
+ 0.291139,
+ 76.4986,
+ 3.2669,
+ 21.1347,
+ 8064.47,
+ 37.4146,
+ 438.561,
+ 0.38055,
+ 11.2435,
+ 0.88877,
+ 1491.72,
+ 4786.46,
+ 867.185,
+ 7.30535,
+ 2.78194,
+ 559.819,
+ 3.69124,
+ 0.523401,
+ 0.474327,
+ 0.929315,
+ 0.722466,
+ 111.985,
+ 1.1903,
+ 1.47662,
+ 0.285894,
+ 35.2424,
+ 0.700978,
+ 419.301,
+ 25760.2,
+ 2.5859,
+ 1.31373,
+ 24.5161,
+ 4.35937,
+ 457.339,
+ 2.59279,
+ 15205,
+ 0.64947,
+ 1.1555,
+ 261.917,
+ 0.252222,
+ 0.443106,
+ 0.376111,
+ 1.0948)
+
+ o2 <- c(3.09828,
+ 8.68183,
+ 272.248,
+ 80.5532,
+ 3.17143,
+ 2813.75,
+ 252.489,
+ 15776.6,
+ 55.5334,
+ 7.92421,
+ 134.694,
+ 92.8906,
+ 8.70729,
+ 0.88829,
+ 2313.62,
+ 5647.12,
+ 121.991,
+ 157.827,
+ 0.411342,
+ 2.28061,
+ 2.82815,
+ 2.02179,
+ 2007.42,
+ 8399.07,
+ 1.32179,
+ 479.284,
+ 30.1469,
+ 1354.44,
+ 7.04809,
+ 0.688492,
+ 45.6092,
+ 16.2209,
+ 0.655503,
+ 64.66,
+ 2.49032,
+ 23.6616,
+ 8801.15,
+ 37.5889,
+ 402.614,
+ 0.792792,
+ 13.1838,
+ 1.30589,
+ 1546.73,
+ 5024.49,
+ 870.876,
+ 6.57147,
+ 3.05968,
+ 568.894,
+ 3.72397,
+ 0.650601,
+ NA,
+ 0.970407,
+ 0.902928,
+ 107.726,
+ NA,
+ 1.74165,
+ 0.15758,
+ 42.8825,
+ 0.632109,
+ 436.377,
+ 27119.4,
+ 4.50098,
+ 0.297246,
+ 18.5351,
+ 2.64522,
+ 490.524,
+ 1.45904,
+ 15831,
+ 0.729047,
+ 0.449076,
+ 277.903,
+ 2.34995,
+ 0.385306,
+ 0.864491,
+ 0.944744)
+
+ o3 <- c(5.78108,
+ 8.41477,
+ 261.53,
+ 71.0515,
+ 2.22543,
+ 2554.46,
+ 235.358,
+ 14074.1,
+ 52.9666,
+ 5.93463,
+ 130.117,
+ 89.6172,
+ 13.3467,
+ 2.71212,
+ 2186.4,
+ 5142.73,
+ 122.094,
+ 202.948,
+ 3.26205,
+ 3.628,
+ 2.82539,
+ 1.14586,
+ 1921.63,
+ 7459.34,
+ 0.987163,
+ 469.363,
+ 27.2883,
+ 1303.06,
+ 10.1981,
+ 1.0284,
+ 44.2452,
+ 14.9583,
+ 1.95817,
+ 62.0998,
+ 4.66003,
+ 24.9048,
+ 7705.65,
+ 39.1692,
+ 377.697,
+ 1.70661,
+ 12.2224,
+ 2.68944,
+ 1432.93,
+ 4672.95,
+ 821.054,
+ 6.00481,
+ 2.91698,
+ 549.193,
+ 6.69091,
+ 2.97898,
+ 1.91727,
+ 3.08212,
+ 2.09839,
+ 113.618,
+ 2.05095,
+ 4.40774,
+ 1.82189,
+ 36.1417,
+ 4.30722,
+ 410.602,
+ 23843.5,
+ 6.58454,
+ 1.3233,
+ 22.6614,
+ 6.2324,
+ 443.329,
+ 1.81664,
+ 14447.8,
+ 2.18542,
+ 0.148822,
+ 237.506,
+ 2.7184,
+ 2.3283,
+ 2.68241,
+ 3.31801)
+
+ return (data.frame(Input=input, Observed1=o1, Observed2=o2, Observed3=o3))
+ }
>
> test.PlotLinear_1 <- function()
+ {
+ x <- .test.data()
+ r <- plotLinear(row.names(x),
+ log2(x$Input),
+ log2(x$Observed1))
+
+ checkEqualsNumeric(r$LOQ$model$breaks, 0.9170727)
+ }
>
> test.PlotLinear_2 <- function()
+ {
+ x <- .test.data()
+ r <- plotLinear(row.names(x),
+ log2(x$Input),
+ log2(x[,c(2:4)]))
+
+ checkEqualsNumeric(r$LOQ$model$breaks, 1.917068888)
+ }
>
> test.PlotLinear_3 <- function()
+ {
+ x <- "15.1062,
+ 15.1062,
+ 241.699,
+ 0.472069,
+ 120.85,
+ 483.398,
+ 0.0590086,
+ 483.398,
+ 15.1062,
+ 241.699,
+ 60.4248,
+ 120.85,
+ 120.85,
+ 0.472069,
+ 0.118017,
+ 0.0590086,
+ 0.944138,
+ 0.118017,
+ 7.5531,
+ 3.77655,
+ 0.236034,
+ 60.4248,
+ 1.88828,
+ 241.699,
+ 0.118017,
+ 0.236034,
+ 0.472069,
+ 30.2124,
+ 241.699,
+ 60.4248,
+ 0.944138,
+ 0.944138,
+ 0.118017,
+ 1.88828,
+ 60.4248,
+ 60.4248,
+ 0.944138,
+ 1.88828,
+ 0.472069,
+ 0.944138,
+ 15.1062,
+ 7.5531,
+ 15.1062,
+ 0.472069,
+ 15.1062,
+ 60.4248,
+ 7.5531,
+ 30.2124,
+ 30.2124,
+ 0.0590086,
+ 0.236034,
+ 0.0590086,
+ 241.699,
+ 0.236034,
+ 30.2124,
+ 120.85,
+ 0.118017,
+ 120.85,
+ 1.88828,
+ 7.5531,
+ 30.2124,
+ 483.398,
+ 7.5531,
+ 966.797,
+ 3.77655,
+ 241.699,
+ 3.77655,
+ 3.77655,
+ 3.77655,
+ 0.236034,
+ 1.88828,
+ 0.0590086"
+
+ y <- "2292.02,
+ 1728.11,
+ 33095.9,
+ 51.557,
+ 13616.2,
+ 54615.3,
+ 5.75489,
+ 60652.2,
+ 1205.27,
+ 30255,
+ 7645.25,
+ 11118.4,
+ 16529.2,
+ 48.5283,
+ 12.6669,
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+ 96.6785,
+ 14.3095,
+ 1151.03,
+ 481.086,
+ 22.5602,
+ 9128.84,
+ 203.783,
+ 24093.9,
+ 15.2307,
+ 22.7496,
+ 50.3159,
+ 4104.9,
+ 19207.5,
+ 6752.21,
+ 123.603,
+ 187.043,
+ 14.0419,
+ 263.462,
+ 3310.3,
+ 8270.03,
+ 119.862,
+ 280.256,
+ 1e-05,
+ 115.157,
+ 2042.86,
+ 1084.78,
+ 1773.62,
+ 54.5923,
+ 1733.97,
+ 6365.94,
+ 901.141,
+ 4224.51,
+ 3612.83,
+ 14.9924,
+ 29.9387,
+ 5.04516,
+ 30960.8,
+ 35.6649,
+ 3664.05,
+ 17094.3,
+ 13.5061,
+ 13986.2,
+ 248.781,
+ 918.314,
+ 3502.82,
+ 64966.4,
+ 860.103,
+ 3426.51,
+ 515.013,
+ 32569.1,
+ 609.002,
+ 427.186,
+ 677.121,
+ 25.5264,
+ 199.22,
+ 8.10828"
+
+ z <- "R1_101,
+ R1_102,
+ R1_11,
+ R1_12,
+ R1_13,
+ R1_14,
+ R1_21,
+ R1_22,
+ R1_23,
+ R1_31,
+ R1_32,
+ R1_33,
+ R1_41,
+ R1_42,
+ R1_43,
+ R1_51,
+ R1_52,
+ R1_53,
+ R1_61,
+ R1_62,
+ R1_63,
+ R1_71,
+ R1_72,
+ R1_73,
+ R1_81,
+ R1_82,
+ R1_83,
+ R1_91,
+ R1_92,
+ R1_93,
+ R2_1,
+ R2_105,
+ R2_115,
+ R2_116,
+ R2_117,
+ R2_140,
+ R2_143,
+ R2_151,
+ R2_152,
+ R2_153,
+ R2_154,
+ R2_18,
+ R2_19,
+ R2_20,
+ R2_24,
+ R2_26,
+ R2_27,
+ R2_28,
+ R2_32,
+ R2_33,
+ R2_37,
+ R2_38,
+ R2_41,
+ R2_42,
+ R2_45,
+ R2_46,
+ R2_47,
+ R2_53,
+ R2_55,
+ R2_57,
+ R2_59,
+ R2_6,
+ R2_60,
+ R2_63,
+ R2_65,
+ R2_66,
+ R2_67,
+ R2_68,
+ R2_71,
+ R2_72,
+ R2_73,
+ R2_76"
+
+ r <- plotLinear(unlist(strsplit(z, split=',')),
+ log2(as.numeric(unlist(strsplit(x, split=',')))),
+ log2(as.numeric(unlist(strsplit(y, split=',')))),
+ showLOQ=TRUE)
+
+ checkEquals(NULL, r$LOQ)
+ }
>
> test.PlotLinear_4 <- function()
+ {
+ x <- "10.0708,
+ 5.0354,
+ 0.8886,
+ 14.2176,
+ 107.422,
+ 859.375,
+ 161.133,
+ 80.5664,
+ 1.7772,
+ 28.4352,
+ 5156.25,
+ 2578.12,
+ 483.398,
+ 3437.5,
+ 27500,
+ 53.7109,
+ 429.688,
+ 0.8886,
+ 14.2176,
+ 483.398,
+ 26.8555,
+ 214.844,
+ 3.5544,
+ 56.8704,
+ 0.0786781,
+ 0.0393391,
+ 454.963,
+ 7279.41,
+ 5156.25,
+ 2578.12,
+ 13.4277,
+ 107.422,
+ 966.797,
+ 966.797,
+ 0.629425,
+ 0.314713,
+ 120.85,
+ 0.4443,
+ 7.1088,
+ 2.5177,
+ 1.25885,
+ 227.482,
+ 3639.71,
+ 7734.38,
+ 7734.38,
+ 1.25885,
+ 0.629425,
+ 1289.06,
+ 644.531,
+ 60.4248,
+ 60.4248,
+ 3750,
+ 117.188,
+ 20.1416,
+ 10.0708,
+ 0.0143051,
+ 0.457764,
+ 120.85,
+ 120.85,
+ 30.2124,
+ 30.2124,
+ 80.5664,
+ 40.2832,
+ 0.269754,
+ 0.539507,
+ 1.07901,
+ 30.2124,
+ 30.2124,
+ 60.4248,
+ 2209.82,
+ 4419.64,
+ 8839.29,
+ 58.5938,
+ 1875,
+ 0.269754,
+ 0.539507,
+ 1.07901,
+ 15.1062,
+ 15.1062,
+ 0.134877,
+ 0.269754,
+ 0.539507,
+ 1933.59,
+ 1933.59,
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+ 7734.38,
+ 2578.12,
+ 1289.06,
+ 0.944138,
+ 20.1416,
+ 10.0708,
+ 1.67847,
+ 13.4277,
+ 1875,
+ 58.5938,
+ 0.839233,
+ 6.71387,
+ 0.0674384,
+ 0.134877,
+ 0.269754,
+ 0.0674384,
+ 0.134877,
+ 0.269754,
+ 0.0674384,
+ 0.134877,
+ 161.133,
+ 80.5664,
+ 0.0337192,
+ 0.134877,
+ 0.0314713,
+ 0.0629425,
+ 0.125885,
+ 0.25177,
+ 0.0168596,
+ 0.0674384,
+ 80.5664,
+ 40.2832,
+ 0.0168596,
+ 0.0337192,
+ 0.0674384,
+ 322.266,
+ 161.133,
+ 937.5,
+ 30000,
+ 0.4443,
+ 7.1088,
+ 0.134877,
+ 0.269754,
+ 0.4443,
+ 7.1088,
+ 29.2969,
+ 937.5,
+ 3.77655,
+ 937.5,
+ 30000,
+ 3.77655,
+ 0.114441,
+ 3.66211,
+ 28.4352,
+ 454.963,
+ 0.114441,
+ 3.66211,
+ 0.0157356,
+ 0.0314713,
+ 0.0629425,
+ 0.125885,
+ 0.0572205,
+ 1.83105,
+ 29.2969,
+ 937.5"
+
+ y1 <- "0.837485,
+ 0.121353,
+ 0.0379273,
+ 0.768669,
+ 1.90631,
+ 0.744164,
+ 1.0572e-06,
+ 3.87601,
+ 8.51e-08,
+ 0.779118,
+ 214.214,
+ 1091.49,
+ 54.3986,
+ 380.045,
+ 0.15194,
+ 2.09719,
+ 17.9671,
+ 0.0795291,
+ 0.478201,
+ 3.56595,
+ 2.38232,
+ 15.8246,
+ 0.394103,
+ 0.895861,
+ 8.8e-09,
+ 0.0712489,
+ 35.6487,
+ 614.35,
+ 988.259,
+ 178.257,
+ 0.532468,
+ 3.26565,
+ 44.7566,
+ 41.5003,
+ 0.0639191,
+ NA,
+ 4.2057,
+ 4.25e-08,
+ 0.596072,
+ 0.232307,
+ 0.0675099,
+ 2.28788,
+ 423.966,
+ 3907.65,
+ 3567.12,
+ 0.111393,
+ 3.9771e-06,
+ 133.993,
+ 154.723,
+ 4.34212,
+ 0.996274,
+ 85.0451,
+ 4.61353,
+ 0.163091,
+ 0.379198,
+ NA,
+ 0.038774,
+ 3.21766,
+ 15.0352,
+ 1.38579,
+ 1.93683,
+ 9.35673,
+ 5.451,
+ 5e-08,
+ 0.0649624,
+ 0.384407,
+ 3.77595,
+ 7.44824,
+ 16.0071,
+ 270.303,
+ 3.494e-07,
+ 1671.87,
+ 6.812,
+ 325.095,
+ 3.935e-07,
+ 0.0616513,
+ 0.0305549,
+ 0.149523,
+ 0.726862,
+ 0.103768,
+ 1.596e-06,
+ 0.0463446,
+ 199.256,
+ 322.444,
+ 1093.72,
+ 1688.88,
+ 279.584,
+ 63.5678,
+ 0.110435,
+ 1.93013,
+ 0.374583,
+ 0.218183,
+ 1.74819,
+ 85.852,
+ 1.21e-08,
+ 0.377331,
+ 1.96912,
+ NA,
+ NA,
+ NA,
+ 0.130965,
+ 1.18e-08,
+ 2.91e-08,
+ NA,
+ NA,
+ 15.1834,
+ 9.38777,
+ NA,
+ 0.0799122,
+ 2.10385e-05,
+ NA,
+ 0.083846,
+ NA,
+ 0.0171778,
+ NA,
+ 3.35384,
+ 5.73421,
+ 5.8264e-06,
+ 6.246e-07,
+ 0.0200194,
+ 17.5116,
+ 11.0122,
+ 260.919,
+ 3964.2,
+ 0.100965,
+ 1.11491,
+ 0.0259428,
+ NA,
+ 0.288957,
+ 0.4821,
+ 1.20828,
+ 193.558,
+ 0.536125,
+ 187.495,
+ 7064.26,
+ 0.264505,
+ 0.0221402,
+ 0.396147,
+ 3.55531,
+ 73.5915,
+ NA,
+ NA,
+ 9.9647e-06,
+ 4.63e-08,
+ 4.7e-09,
+ 0.0237112,
+ 0.0392847,
+ 0.0456551,
+ 1.70831,
+ 91.1479"
+
+ y2 <- "0.722778,
+ 0.733873,
+ 5.219e-07,
+ 0.604539,
+ 1.73717,
+ 1.1534,
+ 1.9165e-06,
+ 3.91994,
+ 4.754e-07,
+ 0.898643,
+ 207.593,
+ 1121.36,
+ 54.4085,
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+ 0.169796,
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+ 16.8435,
+ 0.0616389,
+ 0.619896,
+ 3.89005,
+ 2.5968,
+ 16.6549,
+ 0.182859,
+ 0.948602,
+ 1.016e-07,
+ 0.0403375,
+ 39.1606,
+ 609.005,
+ 1008.73,
+ 157.116,
+ 0.234875,
+ 3.39922,
+ 42.6545,
+ 40.196,
+ 0.181165,
+ 2.847e-07,
+ 4.69883,
+ NA,
+ 0.189675,
+ 0.254871,
+ 0.391466,
+ 2.41451,
+ 426.951,
+ 3810.71,
+ 3577.81,
+ 0.0420185,
+ 4.103e-06,
+ 120.872,
+ 150.976,
+ 4.00902,
+ 1.09308,
+ 88.7421,
+ 4.36902,
+ 0.325112,
+ 0.487459,
+ 0.0794166,
+ 7.003e-07,
+ 3.75052,
+ 13.7295,
+ 1.36716,
+ 2.148,
+ 8.88517,
+ 5.73348,
+ 0.00058588,
+ 0.351373,
+ 0.329472,
+ 4.29572,
+ 7.05352,
+ 18.2358,
+ 266.712,
+ 3.379e-07,
+ 1650,
+ 6.13767,
+ 312.299,
+ NA,
+ 0.0414129,
+ NA,
+ 0.158325,
+ 1.03642,
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+ 0.0904658,
+ 195.812,
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+ 1161.1,
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+ NA,
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+ 0.427896,
+ 3.555e-07,
+ 2.10418,
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+ 6.00372e-05,
+ 0.0432046,
+ NA,
+ 2.8e-06,
+ 1e-10,
+ 0.0702308,
+ NA,
+ NA,
+ 15.5818,
+ 8.15287,
+ NA,
+ 0.089151,
+ 0.0283771,
+ 1.102e-07,
+ 1.27e-08,
+ 3.0816e-06,
+ NA,
+ 0.0412629,
+ 3.26266,
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+ NA,
+ NA,
+ NA,
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+ 0.319625,
+ 0.436569,
+ 1.04639,
+ 191.152,
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+ 0.392405,
+ 2.306e-07,
+ 0.334322,
+ 2.50338,
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+ 0.0358907,
+ 0.350269,
+ 3.09e-08,
+ 2.8e-09,
+ 0.0405143,
+ 9.942e-07,
+ NA,
+ 0.010433,
+ 1.02221,
+ 95.2976"
+
+ y3 <- "0.490311,
+ 0.469879,
+ 0.16225,
+ 0.490533,
+ 2.13129,
+ 1.0798,
+ 2.2654e-06,
+ 4.24638,
+ 0.110956,
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+ 0.088615,
+ 1.34844,
+ NA,
+ NA,
+ 43.9125,
+ 605.221,
+ 1007.06,
+ 177.07,
+ 0.554892,
+ 3.52786,
+ 40.612,
+ 46.9536,
+ 2.0762e-06,
+ 0.0886553,
+ 4.04549,
+ 0.060803,
+ 0.413782,
+ 0.11363,
+ NA,
+ 2.72187,
+ 429.049,
+ 3861.91,
+ 3759.93,
+ 0.108981,
+ 3.9713e-06,
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+ NA,
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+ NA,
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+ 0.911175,
+ NA,
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+ 0.172833,
+ 1.6133,
+ 89.5909,
+ 2.87e-08,
+ 0.496378,
+ 1.83563,
+ 1.506e-07,
+ NA,
+ 0.137899,
+ NA,
+ NA,
+ NA,
+ 0.0146193,
+ 0.0325043,
+ 14.8062,
+ 7.7748,
+ 0.0247236,
+ NA,
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+ NA,
+ 0.0305807,
+ 0.0408539,
+ 0.0168537,
+ NA,
+ 3.43573,
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+ NA,
+ NA,
+ 0.0196412,
+ 17.5211,
+ 11.9901,
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+ 0.907263,
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+ NA,
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+ NA,
+ NA,
+ NA,
+ NA,
+ NA,
+ NA,
+ NA,
+ 0.0269071,
+ 2.66745,
+ 97.6445"
+
+ z <- "R1_101_1,
+ R1_101_2,
+ R1_102_1,
+ R1_102_2,
+ R1_103_1,
+ R1_103_2,
+ R1_11_1,
+ R1_11_2,
+ R1_12_1,
+ R1_12_2,
+ R1_13_1,
+ R1_13_2,
+ R1_14_1,
+ R1_21_1,
+ R1_21_2,
+ R1_22_1,
+ R1_22_2,
+ R1_23_1,
+ R1_23_2,
+ R1_24_1,
+ R1_31_1,
+ R1_31_2,
+ R1_32_1,
+ R1_32_2,
+ R1_33_1,
+ R1_33_2,
+ R1_41_1,
+ R1_41_2,
+ R1_42_1,
+ R1_42_2,
+ R1_43_1,
+ R1_43_2,
+ R1_51_1,
+ R1_51_2,
+ R1_52_1,
+ R1_52_2,
+ R1_53_1,
+ R1_61_1,
+ R1_61_2,
+ R1_62_1,
+ R1_62_2,
+ R1_63_1,
+ R1_63_2,
+ R1_71_1,
+ R1_71_2,
+ R1_72_1,
+ R1_72_2,
+ R1_73_1,
+ R1_73_2,
+ R1_81_1,
+ R1_81_2,
+ R1_82_1,
+ R1_82_2,
+ R1_83_1,
+ R1_83_2,
+ R1_91_1,
+ R1_91_2,
+ R1_92_1,
+ R1_92_2,
+ R1_93_1,
+ R1_93_2,
+ R2_115_1,
+ R2_115_2,
+ R2_116_1,
+ R2_116_2,
+ R2_116_3,
+ R2_117_1,
+ R2_117_3,
+ R2_140_1,
+ R2_14_1,
+ R2_14_2,
+ R2_14_3,
+ R2_150_1,
+ R2_150_2,
+ R2_151_1,
+ R2_151_2,
+ R2_151_3,
+ R2_152_1,
+ R2_152_2,
+ R2_153_1,
+ R2_153_2,
+ R2_153_3,
+ R2_154_1,
+ R2_154_2,
+ R2_18_1,
+ R2_18_2,
+ R2_19_1,
+ R2_19_2,
+ R2_1_1,
+ R2_20_1,
+ R2_20_2,
+ R2_24_1,
+ R2_24_2,
+ R2_26_1,
+ R2_26_2,
+ R2_27_1,
+ R2_27_2,
+ R2_28_1,
+ R2_28_2,
+ R2_28_3,
+ R2_32_1,
+ R2_32_2,
+ R2_32_3,
+ R2_37_2,
+ R2_37_3,
+ R2_41_1,
+ R2_41_2,
+ R2_42_1,
+ R2_42_3,
+ R2_45_1,
+ R2_45_2,
+ R2_45_3,
+ R2_45_4,
+ R2_46_1,
+ R2_46_3,
+ R2_47_1,
+ R2_47_2,
+ R2_53_1,
+ R2_53_2,
+ R2_53_3,
+ R2_54_1,
+ R2_54_2,
+ R2_55_2,
+ R2_55_3,
+ R2_57_1,
+ R2_57_2,
+ R2_59_2,
+ R2_59_3,
+ R2_60_1,
+ R2_60_2,
+ R2_63_1,
+ R2_63_3,
+ R2_65_1,
+ R2_66_1,
+ R2_66_2,
+ R2_67_1,
+ R2_68_1,
+ R2_68_2,
+ R2_6_1,
+ R2_6_2,
+ R2_71_1,
+ R2_71_2,
+ R2_72_1,
+ R2_72_2,
+ R2_72_3,
+ R2_72_4,
+ R2_73_1,
+ R2_73_2,
+ R2_7_1,
+ R2_7_2"
+
+ x <- log2(suppressWarnings(as.numeric(unlist(strsplit(x, split=',')))))
+ y1 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y1, split=',')))))
+ y2 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y2, split=',')))))
+ y3 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y3, split=',')))))
+ z <- unlist(strsplit(z, split=','))
+
+ r <- plotLinear(c(z),
+ x,
+ data.frame(y1=y1, y2=y2, y3=y3),
+ showLOQ=TRUE, showSD=TRUE)
+
+ checkEqualsNumeric(0.8296060465, r$LOQ$model$breaks)
+ }
>
> test.PlotLinear_1()
[1] TRUE
> test.PlotLinear_2()
[1] TRUE
> test.PlotLinear_3()
[1] TRUE
> test.PlotLinear_4()
[1] TRUE
>
> proc.time()
user system elapsed
9.414 0.199 9.682
Anaquin.Rcheck/tests/tPlotLOD.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # Copyright (C) 2016 - Garvan Institute of Medical Research
> #
> # Ted Wong, Bioinformatic Software Engineer at Garvan Institute
> #
>
> library(RUnit)
> library(Anaquin)
Loading required package: ggplot2
>
> test.PlotLOD_1 <- function()
+ {
+ data(UserGuideData_5.6.3)
+ data <- UserGuideData_5.6.3
+
+ xlab <- 'Average Counts'
+ ylab <- 'P-value'
+ title <- 'LODR Curves'
+
+ r <- plotLOD(measured = data$Mean,
+ ratio = data$ExpLFC,
+ pval = data$Pval,
+ qval = data$Qval,
+ xlab = xlab,
+ ylab = ylab,
+ title = title,
+ FDR = 0.1)
+
+ checkEquals(0, r[1,1])
+ checkTrue(is.infinite(r[1,2]))
+ checkEquals(1, r[2,1])
+ checkEqualsNumeric(3.617511181, r[2,2])
+ checkEquals(2, r[3,1])
+ checkEqualsNumeric(5.673070227, r[3,2])
+ checkEquals(3, r[4,1])
+ checkEqualsNumeric(2.584552757, r[4,2])
+ checkEquals(4, r[5,1])
+ checkEqualsNumeric(3.896317229, r[5,2])
+ }
>
> test.PlotLOD_1()
[1] "Threshold: 0.0330366"
| | Ratio| LODR|
|:--|-----:|--------:|
|2 | 1| 3.617511|
|3 | 2| 5.673070|
|4 | 3| 2.584553|
|5 | 4| 3.896317|
[1] TRUE
Warning messages:
1: Transformation introduced infinite values in continuous y-axis
2: Transformation introduced infinite values in continuous y-axis
>
> proc.time()
user system elapsed
2.205 0.162 2.363
Anaquin.Rcheck/tests/tPlotLogistic.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # Copyright (C) 2016 - Garvan Institute of Medical Research
> #
> # Ted Wong, Bioinformatic Software Engineer at Garvan Institute
> #
>
> library(RUnit)
> library(Anaquin)
Loading required package: ggplot2
>
> test.PlotLogistic_1 <- function()
+ {
+ data(UserGuideData_5.4.5.1)
+ x <- UserGuideData_5.4.5.1
+
+ r <- plotLogistic(row.names(x),
+ log2(x$Input),
+ x$Sn)
+
+ # Expected fitted values by the sigmoid function
+ fitted <- c(0.505755856395065,
+ 0.222643528893781,
+ 0.010300016219899,
+ 0.648997187338457,
+ 0.92026304251071,
+ 0.928213869071803,
+ 0.924632245089082,
+ 0.914366418394931,
+ 0.0378973207098846,
+ 0.833752363429975,
+ 0.928358782240202,
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+ 0.927796005796745,
+ 0.010300016219899,
+ 0.648997187338457,
+ 0.927911002760357,
+ 0.823993501178706,
+ 0.926214306703906,
+ 0.129043885951807,
+ 0.901398794826717,
+ 9.82865701336804e-05,
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+ 1.92634758951033e-05,
+ 0.838521261207461,
+ 0.928236933392859)
+
+ checkEquals(r$LOA, 3.33)
+ #all(checkEqualsNumeric(fitted, r$fitted))
+ }
>
> test.PlotLogistic_2 <- function()
+ {
+ data(UserGuideData_5.4.6.3)
+ x <- UserGuideData_5.4.6.3
+
+ checkException(plotLogistic(row.names(data),
+ log2(data$Input),
+ log2(data$Observed1)))
+ }
>
> test.PlotLogistic_1()
[1] TRUE
> test.PlotLogistic_2()
Error in data$Input : object of type 'closure' is not subsettable
[1] TRUE
>
> proc.time()
user system elapsed
2.646 0.144 2.781
Anaquin.Rcheck/tests/tPlotROC.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> #
> # Copyright (C) 2016 - Garvan Institute of Medical Research
> #
> # Ted Wong, Bioinformatic Software Engineer at Garvan Institute
> #
>
> library(RUnit)
> library(Anaquin)
Loading required package: ggplot2
>
> test.PlotROC_1 <- function()
+ {
+ data(UserGuideData_5.6.3)
+ x <- UserGuideData_5.6.3
+ x$label <- ifelse(abs(x$ExpLFC) <= 0, 'FP', 'TP')
+
+ r <- plotROC(row.names(x),
+ 1-x$Pval,
+ abs(x$ExpLFC),
+ x$label,
+ refGroup=0)
+
+ checkEquals(as.character(r$AUC[1,][1]), '4')
+ checkEqualsNumeric(r$AUC[1,]$AUC, 0.9062)
+ checkEquals(as.character(r$AUC[2,][1]), '3')
+ checkEqualsNumeric(r$AUC[2,]$AUC, 0.8939)
+ checkEquals(as.character(r$AUC[3,][1]), '2')
+ checkEqualsNumeric(r$AUC[3,]$AUC, 0.7955)
+ checkEquals(as.character(r$AUC[4,][1]), '1')
+ checkEqualsNumeric(r$AUC[4,]$AUC, 0.6713)
+ }
>
> test.PlotROC_1()
| | AUC|
|--:|------:|
| 4| 0.9062|
| 3| 0.8939|
| 2| 0.7955|
| 1| 0.6713|
[1] TRUE
>
> proc.time()
user system elapsed
1.912 0.144 2.041
Anaquin.Rcheck/Anaquin-Ex.timings
| name | user | system | elapsed | |
| plotLOD | 0.806 | 0.043 | 0.860 | |
| plotLinear | 1.729 | 0.018 | 1.773 | |
| plotLogistic | 1.442 | 0.009 | 1.470 | |
| plotROC | 0.480 | 0.004 | 0.489 | |