Changes in version 1.21.7
BUG FIXES
- Noticed an issue with GenomicState::gencode_genomic_state() that
ultimately was due to makeGenomicState() and the transition in R to
have as default data.frame(stringsAsFactors = FALSE) instead of
TRUE.
Changes in version 1.21.5
SIGNIFICANT USER-VISIBLE CHANGES
- Now makeGenomicState() now restores the
GenomicFeatures::isActiveSeq() on the txdb object before finishing
to avoid issues, like running regionReport::renderReport() on two
different sets of regions (different chrs). There's a new unit test
for this.
BUG FIXES
- Removed knitrBootstrap citation code.
- Made a test less susceptible to numerical precision.
Changes in version 1.21.2
SIGNIFICANT USER-VISIBLE CHANGES
- Documentation website is now available at
http://lcolladotor.github.io/derfinder/. It gets updated with every
commit on the master branch (bioc-devel) using GitHub Actions and
pkgdown.
Changes in version 1.21.1
SIGNIFICANT USER-VISIBLE CHANGES
- Use GenomeInfoDb::getChromInfoFromUCSC() when possible instead of
data from biovizBase::hg19Ideogram for getting the hg19 chromosome
lengths.
Changes in version 1.19.9
BUG FIXES
- Fixed an important bug in findRegions() that affected the end
positions of the regions when maxRegionGap was supplied with a value
greater than the default of 0 and the data was filtered (so position
was not all TRUE in the findRegions() call). To check this scenario
now there is a new unit test under
tests/testthat/test-maxRegionGap.R.
- The above bug went unnoticed in getRegionCoverage() and thus for
regionMatrix() for the same type of situations (filtered data with a
non-zero maxRegionGap). The coverage values are ok, it's just the
end positions of the regions returned by findRegions() that were
incorrect and that would need to be re-computed with the fixed
version.
- Changed some internal tests to check bumphunter::loessByCluster()
instead of bumphunter::runmedByCluster() given some issues with the
second one.
Changes in version 1.19.8
- Added a NEWS.md file to track changes to the package.
Changes in version 1.19.4
BUG FIXES
- railMatrix() and loadCoverage() helper functions had an issue when
the input set of regions was duplicated. This could be reproduced
with
sampleFile <- c('SRR387777' = 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw')
regs <- GenomicRanges::GRanges('chrY', IRanges(start = c(1, 1), width = 10), strand = '-')
names(regs) <- c(1:2)
result <- rtracklayer::import(sampleFile, selection = regs, as = 'RleList')
This error affected recount and other reverse dependencies that use
derfinder for processing BigWig files.
Changes in version 1.19.2
BUG FIXES
- railMatrix() and loadCoverage() helper functions now attempt to
import a BigWig file 3 times before giving up. Based on
http://bioconductor.org/developers/how-to/web-query/ and
https://github.com/leekgroup/recount/commit/8da982b309e2d19638166f263057d9f85bb64e3f
which will make these functions more robust to occasional web access
issues.
Changes in version 1.17.3
NEW FEATURES
- Add ORCID's following changes at
http://bioconductor.org/developers/package-guidelines/#description
Changes in version 1.17.2
BUG FIXES
- Use R's random seeds from version 3.5.0 for the test thanks to
https://twitter.com/StrictlyStat/status/1103303028751372289
Changes in version 1.15.4
SIGNIFICANT USER-VISIBLE CHANGES
- Switched from outfile to log when invoking
BiocParallel::SnowParam(). Thus define_cluster() now has a mc.log
argument instead of mc.outfile.
Changes in version 1.15.2
BUG FIXES
- Fix a message regarding the deprecated IRanges subset method.
Changes in version 1.15.1
SIGNIFICANT USER-VISIBLE CHANGES
- Use BiocManager
Changes in version 1.13.8
BUG FIXES
- Fixed a unit test that was breaking version 1.13.7.
Changes in version 1.13.1
NEW FEATURES
- Added an extra example to regionMatrix() in response to
https://support.bioconductor.org/p/103591
Changes in version 1.11.8
BUG FIXES
- Improved the documentation regarding an error when
coverageInfo$position is NULL when running analyzeChr() and
indirectly running preprocessCoverage(). See
https://support.bioconductor.org/p/99400/ for details.
Changes in version 1.11.7
SIGNIFICANT USER-VISIBLE CHANGES
- Vignette now uses the new BiocStyle::html_document that was recently
released.
Changes in version 1.11.4
BUG FIXES
- regionMatrix() will now pass the hidden arguments species and
currentStyle to getRegionCoverage() so they can be used by
extendedMapSeqlevels(). Related to
https://support.bioconductor.org/p/95721/.
Changes in version 1.11.2
BUG FIXES
- Improved documentation of extendedMapSeqlevels(). Related to
https://support.bioconductor.org/p/95521/.
- Improved filterData() based on
https://github.com/lcolladotor/derfinder/issues/38
Changes in version 1.9.6
BUG FIXES
- Fixed define_cluster() to match recent changes in BiocParallel and
fixed an if clause in regionMatrix() that could lead to warnings in
some situations.
Changes in version 1.9.3
SIGNIFICANT USER-VISIBLE CHANGES
- regionMatrix() now has explicit arguments totalMapped and targetSize
so that users will almost always normalize by library size when
using this function (if they see the help page) or in the steps
prior to using regionMatrix().
Changes in version 1.9.2
BUG FIXES
- Clarified the documentation of mc.cores and mc.cores.load in
fullCoverage() thanks to feedback from Emily E Burke
https://github.com/emilyburke.
Changes in version 1.7.16
SIGNIFICANT USER-VISIBLE CHANGES
- Help pages now document advanced arguments.
- Deprecated advancedArg().
Changes in version 1.7.14
NEW FEATURES
- Added the function getTotalMapped() for calculating the total number
of mapped reads for a BAM file or the area under the curve (AUC) for
a BigWig file. This information can then be used with
fullCoverage(), filterData() and other functions. Note that if you
totalMapped in fullCoverage() you should not use totalMapped again
in filterData().
Changes in version 1.7.12
BUG FIXES
- Updated links to BrainSpan. Issue reported by Steve Semick
https://github.com/SteveSemick.
Changes in version 1.7.2
BUG FIXES
- Now derfinder uses DataFrame(check.names = FALSE) to avoid naming
issues.
Changes in version 1.7.1
SIGNIFICANT USER-VISIBLE CHANGES
- Dropped defunct functions.
Changes in version 1.5.39
BUG FIXES
- annotateRegions() now ignores strand by default.
Changes in version 1.5.37
SIGNIFICANT USER-VISIBLE CHANGES
- The users guide vignette now has a short section explaining how to
use derfinder for differential binding analysis with ChIP-seq data.
Changes in version 1.5.27
SIGNIFICANT USER-VISIBLE CHANGES
- Added smoothing arguments for the single base-level approach based
on functions from the bumphunter package. These arguments are useful
for identifying differentially bounded ChIP-seq peaks.
Changes in version 1.5.13
BUG FIXES
- Fixed railMatrix()'s flexibility for defining the cluster used for
loading the BigWig files. You can now use BPPARAM.railChr which will
take priority over file.cores. Also, if file.cores = 1L, then the
default will be to use SerialParam(), which was the implementation
available prior to 1.5.11.
Changes in version 1.5.11
SIGNIFICANT USER-VISIBLE CHANGES
- Now coverageToExon(), regionMatrix() and railMatrix() can take an L
argument of length equal to the number of samples in case not all
samples have the same read length.
- railMatrix() has a new argument called file.cores for controlling
how many cores are used for loading the BigWig files. In theory this
allows using railMatrix() with BPPARAM.custom equal to a
BiocParallel::BatchJobsParam() to submit 1 job per chromosome, then
file.cores determines the number of cores for reading the files.
This is a highly experimental feature.
Changes in version 1.5.9
SIGNIFICANT USER-VISIBLE CHANGES
- Dropped the old introductory and advanced vignettes. We think that
the new vignettes are clearer. In particular, they do a better job
at highlighting the differences between the expressed regions-level
and single base-level F-statistics implementations of the DER Finder
approach to RNA-seq data.
Changes in version 1.5.8
SIGNIFICANT USER-VISIBLE CHANGES
- Added a users guide vignette which explains nearly every detail you
would want to know as a user.
Changes in version 1.5.7
SIGNIFICANT USER-VISIBLE CHANGES
- Added a quick start vignette.
Changes in version 1.5.6
NEW FEATURES
- Introduced railMatrix() which generates similar output to
regionMatrix() but is much faster and less memory intensive. It
achieves this by extracting the required information from BigWig
files.
Changes in version 1.3.3
SIGNIFICANT USER-VISIBLE CHANGES
- Brought back the mc.outfile argument for specifying the outfile
argument in SnowParam(). See more details at
https://stat.ethz.ch/pipermail/bioc-devel/2015-May/007531.html
Changes in version 1.3.2
SIGNIFICANT USER-VISIBLE CHANGES
- Deprecated functions with underscores in their names in favor of
camelCase functions. This was done to simplify the package.
Changes in version 1.3.1
SIGNIFICANT USER-VISIBLE CHANGES
- Greatly increased the speed of the p-values calculation step. See
https://github.com/lcolladotor/derfinder/issues/29 for details.
Changes in version 1.1.18
BUG FIXES
- Updated to work with qvalue 1.99.0.
Changes in version 1.1.17
SIGNIFICANT USER-VISIBLE CHANGES
- Changed citation information to reference the bioRxiv pre-print.
BUG FIXES
- Polished the interaction with bumphunter >= 1.7.3.
- Updated the default cluster option now that
BiocParallel::SnowParam() no longer has an outfile argument.
Changes in version 1.1.16
SIGNIFICANT USER-VISIBLE CHANGES
- analyzeChr() now uses annotateTranscripts() and matchGenes() from
bumphunter version 1.7.3 (or greater). As announced at
https://support.bioconductor.org/p/63568/ these changes in
bumphunter allow straight forward use of non-human annotation. In
analyzeChr() using a different organism can be used by changing the
txdb argument: finer control can be achieved through .... For
example, by specifying the annotationPackage argument used in
annotateTranscripts().
Changes in version 1.1.15
BUG FIXES
- makeGenomicState() incorrectly labeled regions as intragenic. The
correct name is intergenic.
Changes in version 1.1.14
BUG FIXES
- Fixed an important bug on calculatePvalues()! Basically, internally
maxRegionGap was set to 300 instead of 0 in one step by default.
Thus the process of mapping regions to genomic coordinates was
messed up. If you have results prior to this fix you can try using
https://gist.github.com/bf85e2c7d5d1f8197707 to fix the results as
much as possible. Basically, regions will be correct but the
p-values will be approximated with the available information from
the null regions. Truly fixing the p-values can only be done by
re-running derfinder.
Changes in version 1.1.5
NEW FEATURES
- Introduced function extendedMapSeqlevels() for using GenomeInfoDb
when there is information regarding the species and naming style of
interest. otherwise sequence names are left unchanged. If used with
verbose = TRUE, a message is printed whenever GenomeInfoDb could not
be used or if some information had to be guessed.
BUG FIXES
- Fixes https://support.bioconductor.org/p/62136.
Changes in version 1.1.3
NEW FEATURES
- loadCoverage() and fullCoverage() now support BamFile and BigWigFile
objects.
BUG FIXES
- Fixed a bug in loadCoverage() when the input was a BamFileList.
Implemented tests based on the bug. Bug reported at
https://support.bioconductor.org/p/62073
Changes in version 0.99.0
NEW FEATURES
- Preparing to submit to Bioconductor.
Changes in version 0.0.81
NEW FEATURES
- Added an advanced vignette.
Changes in version 0.0.80
NEW FEATURES
- Introductory vignette completed.
Changes in version 0.0.79
SIGNIFICANT USER-VISIBLE CHANGES
- mergeResults() can now calculate FWER adjusted p-values when
provided with optionsStats. Updated analyzeChr() to supply the
required information.
Changes in version 0.0.78
NEW FEATURES
- Added an introductory vignette.
Changes in version 0.0.77
NEW FEATURES
- Added advancedArg() and its alias advanced_arg() which links to the
docs for the advanced arguments by opening a browser window with the
relevant information from GitHub.
- getRegionCoverage() and coverageToExon() now have the files argument
which is used only when fullCov is NULL. Both functions will attempt
to extract the coverage data from the raw files for the regions of
interest in that case.
Special care has to be taken in order to guarantee that the coverage is
the same as some reads might be discarded if the region is too narrow.
See the advanced argument protectWhich in loadCoverage() for more
information. Also, if totalMapped and targetSize were used prior to
filtering, they should be used again.
- loadCoverage() has new advanced arguments that help when reading a
specific region (or regions) of the genome.
Changes in version 0.0.76
SIGNIFICANT USER-VISIBLE CHANGES
- loadCoverage() and fullCoverage() argument dirs has been renamed to
files for greater consistency with what it represents.
Changes in version 0.0.75
SIGNIFICANT USER-VISIBLE CHANGES
- regionMatrix() now returns the output of getRegionCoverage() so you
don't have to run it twice if you are interested in using
derfinderPlot::plotRegionCoverage().
- regionMatrix()$regions now guesses the seqlengths
BUG FIXES
- Fixed .advanced_argument() to work in nested functions
- Fixed a case in getRegionCoverage() where fullCov$position was
provided but it was NULL.
- Fixed regionMatrix(totalMapped, targetSize) case which would
previously lead to an error in the getRegionCoverage() step.
Changes in version 0.0.74
SIGNIFICANT USER-VISIBLE CHANGES
- Most functions had their arguments changed to increase usability.
Some have advanced arguments inside the code.
Changes in version 0.0.71
SIGNIFICANT USER-VISIBLE CHANGES
- Introduced coerceGR(), createBwSample() and createBw() for exporting
output from fullCoverage() into BigWig files.
Changes in version 0.0.70
SIGNIFICANT USER-VISIBLE CHANGES
- All exported functions now have aliases with underscore names for
those that prefer them over camel case names. For example,
analyze_chr() is the new alias for analyzeChr().
- makeBamList() has been renamed to rawFiles() since it can be used to
identify a list of BigWig files instead of BAM files.
Changes in version 0.0.69
SIGNIFICANT USER-VISIBLE CHANGES
- loadCoverage() and fullCoverage() now have a tilewidth argument.
When specified GenomicFiles is used to read the coverage in chunks.
In theory, this can lead to lower memory usage at the expense of
time.
Changes in version 0.0.67
SIGNIFICANT USER-VISIBLE CHANGES
- preprocessCoverage() now has a toMatrix argument which is only used
when lowMemDir is not NULL. It controls whether to save the chunks
as DataFrame objects or dgCMatrix objects and the idea is that it
can time by just transforming the data once instead of doing so at
each permutation.
Changes in version 0.0.66
SIGNIFICANT USER-VISIBLE CHANGES
- fstats.apply() has been moved to it's own package: derfinderHelper.
This will speed up the run time when using BiocParallel::SnowParam()
as derfinderHelper takes much less time to load than derfinder.
- plotCluster(), plotOverview() and plotRegionCoverage() were all
moved to their new own package: derfinderPlot. This will make
maintenance easier as the dependency ggbio is still under active
development.
Changes in version 0.0.65
- Re-organized code for fstats.apply(). Note that improving
.transformSparseMatrix() would speed up the Matrix method.
- Note that all parallel functions have some overhead from loading
derfinder on each worker. Check system.time(library(derfinder)) to
see how long the overhead is. It only pays off to use more cores if
the calculations are taking longer than the overhead.
Changes in version 0.0.64
SIGNIFICANT USER-VISIBLE CHANGES
- fullCoverage() has several new arguments and now is a full parallel
implementation of loadCoverage(). These changes were introduced
since fullCoverage() no longer blows up in memory since
version 0.0.62 and thus the new recommended use case is to call
fullCoverage() instead of running one job with loadCoverage() per
chromosome or using a lapply() loop.
Changes in version 0.0.63
NEW FEATURES
- fstats.apply() now has method and scalefac arguments. The method
argument controls which of the 3 implementations to use. The old
method is called regular now. The new method Rle calculates the
F-statistics without de-compressing the data, which is good for
memory but gets considerably slower as the number of samples
increases. The default method is Matrix which uses the Matrix
package and is both faster (given that the coercion doesn't take
long) and less memory intensive than the regular method.
SIGNIFICANT USER-VISIBLE CHANGES
- Functions analyzeChr(), calculatePvalues() and calculateStats() now
have arguments method and scalefac to match the changes in
fstats.apply().
Changes in version 0.0.62
NEW FEATURES
- derfinder now uses BiocParallel::blapply() instead of
parallel::mclapply() When mc.cores is greater than 1,
BiocParallel::SnowParam() is used to construct the cluster.
Otherwise, BiocParallel::SerialParam() is used. This change reduces
memory load when using the functions that have the mc.cores argument
greater than 1.
- Functions analyzeChr(), calculatePvalues(), calculateStats(),
coverageToExon(), fullCoverage(), getRegionCoverage(),
regionMatrix() all have a new argument mc.output. This is passed to
BiocParallel::SnowParam(outfile).
SIGNIFICANT USER-VISIBLE CHANGES
- You may now use fullCoverage() without problems and should no longer
encounter errors due to longer vectors not being implemented.
- Functions like fullCoverage() now use much less memory and do not
blow up as you increase mc.cores. Note however that the memory does
increase, but now it`s close to linear.
- Examples might take longer to run with mc.cores greater than 1, but
that is due to the small setup overhead of BiocParallel::SnowParam()
which is minimal compared to the overall speed gains with real data
sets.
Changes in version 0.0.61
SIGNIFICANT USER-VISIBLE CHANGES
- filterData() and loadCoverage() now have arguments totalMapped and
targetSize
- getRegionCoverage() and regionMatrix() can now work with list output
from loadCoverage() with a non-NULL cutoff
- regionMatrix() now has an argument runFilter so it can be used with
previous output from loadCoverage()/filterData() with
returnMean=TRUE
Changes in version 0.0.60
SIGNIFICANT USER-VISIBLE CHANGES
- analyzeChr(), annotateRegions(), calculatePvalues(),
coverageToExon(), findRegions(), fullCoverage(),
getRegionCoverage(), makeGenomicState(), mergeResults(),
plotCluster(), plotOverview() now all have chrsStyle as an argument
to specify the chromosome naming convention used. Defaults to UCSC.
- makeGenomicState() no longer has the addChrPrefix argument. It has
been replaced by chrsStyle to use GenomeInfoDb to set the naming
style.
- chrnums has been renamed to chrs in fullCoverage() and
mergeResults()
- chrnum has been renamed to chr in analyzeChr()
Changes in version 0.0.59
NEW FEATURES
- Updated to work with BioC version 3.0
Changes in version 0.0.58
NEW FEATURES
- loadCoverage() and fullCoverage() can now import data from BigWig
files.
Changes in version 0.0.57
SIGNIFICANT USER-VISIBLE CHANGES
- regionMatrix() now relies on getRegionCoverage() instead of
coverageToExon() making it faster and less memory intensive.
Changes in version 0.0.56
NEW FEATURES
- Added regionMatrix() for filtering coverage data and using the
resulting regions to construct a count matrix. Uses several
derfinder functions.
SIGNIFICANT USER-VISIBLE CHANGES
- Made coverageToExon() more robust for different names in fullCov.
- filterData() and loadCoverage() have new arguments filter,
returnMean, and returnCoverage which allow speeding up
regionMatrix(). preprocessCoverage() was changed accordingly.
- getRegionCoverage() now internally uses USCS names.
BUG FIXES
- Fixed warnings in coverageToExon().
Changes in version 0.0.55
SIGNIFICANT USER-VISIBLE CHANGES
- Added a NEWS file with curated information from the git commit
history.
Changes in version 0.0.54
SIGNIFICANT USER-VISIBLE CHANGES
- Added example data for mergeResults(). Now all functions have
examples.
Changes in version 0.0.53
SIGNIFICANT USER-VISIBLE CHANGES
- Now derfinder includes the genomic state output for hg19 chr21. This
allowed to implement examples for annotateRegions(),
getRegionCoverage(), and coverageToExon().
Changes in version 0.0.52
SIGNIFICANT USER-VISIBLE CHANGES
- Several examples run much faster now
Changes in version 0.0.51
SIGNIFICANT USER-VISIBLE CHANGES
- makeGenomicState() now has an example
Changes in version 0.0.50
BUG FIXES
- Fixed warnings in makeGenomicState() related to changes in
AnnotationDbi
Changes in version 0.0.49
BUG FIXES
- Updated the help for plotRegionCoverage() and fixed an issue.
Changes in version 0.0.48
SIGNIFICANT USER-VISIBLE CHANGES
- loadCoverage() now allows specifying which strand you want to load.
More at https://github.com/lcolladotor/derfinder/issues/16
Changes in version 0.0.47
SIGNIFICANT USER-VISIBLE CHANGES
- getRegionCoverage() now has a depth-adjustment argument
BUG FIXES
- Fixed several bugs as suggested by Andrew Jaffe
Changes in version 0.0.46
SIGNIFICANT USER-VISIBLE CHANGES
- Now requires R version 3.1
- Changed Github organization to match the Git-SVN Bioconductor bridge
guidelines.
- Dropped Rcpp and RcppArmadillo from F-stats calculation. More at
https://github.com/lcolladotor/derfinder/pull/17
- Stored the results from some of the example data to speed up other
examples. Check ?genomeDataRaw, ?genomeFstats, ?genomeRegions
BUG FIXES
- Fixed verbose for getRegionCoverage()
- plotRegionCoverage() now matches latest getRegionCoverage() output
Changes in version 0.0.44
SIGNIFICANT USER-VISIBLE CHANGES
- Updated getRegionCoverage() with a new method for sub setting the
coverage matrices, allowing for coverage estimates from overlapping
regions. Now also uses mclapply().
BUG FIXES
- Fixed NAMESPACE to match current bioc-devel (2.14) as suggested by
Tim Triche.
Changes in version 0.0.42
SIGNIFICANT USER-VISIBLE CHANGES
- A series of performance enhancements were made to reduce the memory
load (albeit a very minor time increase).
BUG FIXES
- Updated analyzeChr() to handle correctly the new lowMemDir argument.
Changes in version 0.0.41
SIGNIFICANT USER-VISIBLE CHANGES
- Introduced the lowMemDir argument to preprocessCoverage(),
calculateStats(), calculatePvalues(), fstats.apply(), and
analyzeChr(). Reduces peak memory usage at the expense of some
input-output.
Changes in version 0.0.40
SIGNIFICANT USER-VISIBLE CHANGES
- mergeResults() will not merge pre-processed data by default
- coverageToExon() now uses mclapply() when possible
Changes in version 0.0.39
SIGNIFICANT USER-VISIBLE CHANGES
- Changed how the data is pre-processed and pre-splitted.
Changes in version 0.0.38
SIGNIFICANT USER-VISIBLE CHANGES
- preprocessCoverage() now uses Reduce() instead of .rowMeans()
Changes in version 0.0.37
SIGNIFICANT USER-VISIBLE CHANGES
- Updated the example in plotCluster()
Changes in version 0.0.36
NEW FEATURES
- Added collapseFullCoverage()
SIGNIFICANT USER-VISIBLE CHANGES
- sampleDepth() has been greatly changed. It is now based on Hector
Corrada`s ideas implemented in metagenomeSeq.
- Updated several man pages.
Changes in version 0.0.35
BUG FIXES
- Fixed an issue with the bumphunter dependency.
Changes in version 0.0.34
BUG FIXES
- Merged changes suggested by Michael Love
Changes in version 0.0.33
BUG FIXES
- Implemented fixes suggested by Michael Love
Changes in version 0.0.32
BUG FIXES
- Fixed an important bug in the F-stats calculation
- Implemented fixes suggested by Michael Love
Changes in version 0.0.31
BUG FIXES
- loadCoverage() now uses readGAlignmentsFromBam()
Changes in version 0.0.30
SIGNIFICANT USER-VISIBLE CHANGES
- Added a bai argument to fullCoverage()
- loadCoverage() can now work with a pre-defined BamFileList object.
Changes in version 0.0.29
SIGNIFICANT USER-VISIBLE CHANGES
- Now requires R version 3.0.2
- Changed the default of center in sampleDepth() to FALSE.
- Added a runAnnotation argument to analyzeChr().
- Added a bai argument to loadCoverage().
- Added an adjustF argument to all stats functions. Useful for cases
when the RSS of the alternative model is very small.
BUG FIXES
- Fixed plotRegionCoverage() and plotCluster() for unexpected cases.
Changes in version 0.0.28
NEW FEATURES
- Added sampleDepth()
SIGNIFICANT USER-VISIBLE CHANGES
- generateReport() has been moved to it's own new package called
derfinderReport. It is available at
https://github.com/lcolladotor/derfinderReport
- Examples and analyzeChr() have been updated now that sampleDepth()
was added
Changes in version 0.0.26
SIGNIFICANT USER-VISIBLE CHANGES
- Renamed package from derfinder2 to derfinder to comply with
Bioconductor guidelines.
Changes in version 0.0.25
SIGNIFICANT USER-VISIBLE CHANGES
- Changed how makeModels() deals with cases when mod and mod0 are not
full rank.
- plotCluster() now no longer depends on an active Internet connection
for hg19 = TRUE.
BUG FIXES
- Fixed minor graphical issues in plotRegionCoverage(), plotCluster()
and in generateReport()
Changes in version 0.0.24
BUG FIXES
- Fixed plotRegionCoverage() for cases when in
annotateRegions(minoverlap=x) lead to no overlaps being found
between a region and annotation.
Changes in version 0.0.23
BUG FIXES
- Fixed some bugs in calculatePvalues() when no null regions or only
some were found.
- Fixed a bug using colsubset on analyzeChr().
- Fixed an issue when the F-stat cutoff used is too high and no
regions are found.
- Fixed an issue when testvars in makeModels() had unused levels.
- Fixed an issue when qvalue::qvalue() fails due to incorrect
estimation of pi0
- Fixed a bug on how the regions were being clustered.
Changes in version 0.0.22
SIGNIFICANT USER-VISIBLE CHANGES
- MA-style plots in generateReport() now weight the mean by the number
of samples in each group. Also removed the mean coverage vs area
section. generateReport() now also has a nBestClusters argument.
- plotCluster() now uses scales and has a forceLarge argument
BUG FIXES
- Fixed an important bug in finding candidate DERs. The example for
plotCluster() now includes code that was used for visualizing the
bug.
- Fixed some NAMESPACE issues
Changes in version 0.0.21
NEW FEATURES
- Added getRegionCoverage(), coverageToExon(), plotRegionCoverage()
SIGNIFICANT USER-VISIBLE CHANGES
- Renamed plotRegion() to plotCluster() plus it no longer shows the
exons track as it is redundant information
- mergeResults() now also runs annotateRegions()
- generateReport() now uses plotRegionCoverage() and includes MA-style
plots
Changes in version 0.0.20
NEW FEATURES
- Added annotateRegions()
Changes in version 0.0.19
NEW FEATURES
- Added makeGenomicState()
Changes in version 0.0.18
NEW FEATURES
- Added fullCoverage()
Changes in version 0.0.17
SIGNIFICANT USER-VISIBLE CHANGES
- preprocessCoverage() now uses the groupInfo argument
- calculatePvalues() now calculates log2 fold changes (without scaling
or adjusting for library size)
- Greatly improved generateReport()
Changes in version 0.0.16
NEW FEATURES
- Added generateReport()
BUG FIXES
- Fixed bugs in mergeResults()
Changes in version 0.0.15
SIGNIFICANT USER-VISIBLE CHANGES
- getSegmentsRle() was greatly simplified
BUG FIXES
- Fixed analyzeChr(), completed mergeResults()
Changes in version 0.0.14
NEW FEATURES
- Added analyzeChr() and mergeResults()
SIGNIFICANT USER-VISIBLE CHANGES
- Updated README.md
- makeModels() now uses testvars instead of group and has a new
arguments groupInfo, center and testIntercept
- calculatePvalues() now uses area of regions instead of mean to
calculate the p-values.
- preprocessCoverage() now calculates the mean coverage at each base
Changes in version 0.0.13
SIGNIFICANT USER-VISIBLE CHANGES
- Users can specify significance cutoffs for plotOverview() and
plotRegion()
Changes in version 0.0.12
SIGNIFICANT USER-VISIBLE CHANGES
- calculatePvalues() now uses qvalue::qvalue() instead of p.adjust()
Changes in version 0.0.11
SIGNIFICANT USER-VISIBLE CHANGES
- Added plotOverview()
Changes in version 0.0.10
SIGNIFICANT USER-VISIBLE CHANGES
- Added plotRegion()
BUG FIXES
- makeModels() can now handle a vector for the adjustvars argument
Changes in version 0.0.9
SIGNIFICANT USER-VISIBLE CHANGES
- calculatePvalues() will adjust the p.values now using p.adjust()
- makeModels() now can handle a matrix for the group argument
BUG FIXES
- getSegmentsRle() will now work properly in the case that no segments
are found
Changes in version 0.0.8
SIGNIFICANT USER-VISIBLE CHANGES
- Attempted to reduce memory load in calculateStats() and
calculatePvalues()
Changes in version 0.0.7
SIGNIFICANT USER-VISIBLE CHANGES
- fstats.apply() now uses Rcpp and RcppArmadillo
Changes in version 0.0.6
NEW FEATURES
- preprocessCoverage() can now automatically select the chunksize
SIGNIFICANT USER-VISIBLE CHANGES
- Dropped fstats() and is now part of fstats.apply()
Changes in version 0.0.5
NEW FEATURES
- Introduced method argument for getSegmetnsRle()
BUG FIXES
- No longer permuting the data matrix in calculatePvalues()
Changes in version 0.0.4
NEW FEATURES
- Added makeBamList(), makeModels(), and preprocessCoverage()
- Added example data from the Montogemery and Pickrell studies. Check
?genomeData and ?genomeInfo
Changes in version 0.0.3
NEW FEATURES
- Added calculatePvalues()
Changes in version 0.0.2
NEW FEATURES
- Added clusterMakerRle(), findRegions(), and getSegmentsRle()
Changes in version 0.0.1
NEW FEATURES
- Added calculateStats(), filterData(), fstats(), and fstats.apply()
SIGNIFICANT USER-VISIBLE CHANGES
- Renamed makeCoverage() to loadCoverage()
- Improved NAMESPACE
Changes in version 0.0.0
NEW FEATURES
- Initialized the package (named derfinder2) from derfinder
https://github.com/alyssafrazee/derfinder version 1.0.2 This version
is available at
https://github.com/alyssafrazee/derfinder/tree/d49f7b28c26f075da36a50ab67c9d192ab2fd63d