NEWS
methylKit 1.33.2
IMPROVEMENTS AND BUG FIXES
- processBismarkAln: fix cigar buffer storage issue which led to faulty methylation calls (#334)
- remove zlibbioc dependency, zlibbioc is now deprecated in Bioc 3.21 and will be removed in Bioc 3.22
methylKit 1.33.1
IMPROVEMENTS AND BUG FIXES
- bedgraph: fix bedgraph error due to NA handling in meth.diff export (#331)
methylKit 1.27.2
IMPROVEMENTS AND BUG FIXES
- fix R-Devel build error:
- issues was caused by S4Vectors::isEmpty
- fixed by replacing S4Vectors::isEmpty with is.null
methylKit 1.27.1
IMPROVEMENTS AND BUG FIXES
- fix R cmd check warnings:
- fix "Undocumented arguments in documentation object" by
documenting ‘...’, ‘treatment’ arguments for methylRawList and
methylRawListDB constructors
- methCall: replace variable length char with vector of chars to fix the
warning: "variable length arrays are a C99 feature [-Wvla-extension]"
- methCall: simplify the parsing of cigar string and replace
calls to deprecated std::sprintf with std::snprintf
- add test for processBismarkAln to check that reading sam and bam
returns the same object for the same content
methylKit 1.17.5
IMPROVEMENTS AND BUG FIXES
- fread.gzipped: skip header rows in tabix file to fix https://github.com/al2na/methylKit/issues/226
methylKit 1.17.4
IMPROVEMENTS AND BUG FIXES
- .setMethylDBNames: correct possible methylDBclass from "methylDB"
to "methylRawDB"
- fread.gzipped: disable skipping of decompression in fread.gzipped
- can cause serious issues as investigated in
https://groups.google.com/g/methylkit_discussion/c/UruFjvX89B4/m/vV2Qnd8NEAAJ
and explained in https://github.com/al2na/methylKit/issues/222
methylKit 1.17.3
IMPROVEMENTS AND BUG FIXES
- export methylRawListDB and methylRawList constructors
methylKit 1.17.2
IMPROVEMENTS AND BUG FIXES
- update vignette:
- add note about use of system.file function
- reduce number of rows, when showing row ordering
- add faq section about merging methylRaw into methylRawList update vignette
methylKit 1.17.1
IMPROVEMENTS AND BUG FIXES
- readmethylDB: check if file exists before trying to read
- loading tabix files:
- improve reading tabix files with header
- update tests for loading tabix files
methylKit 1.15.3
NEW FUNCTIONS AND FEATURES
- add verbosity argument to methCall to allow for
complete silencing of output, this will be set by
processBismarkAln which gained 'verbose' argument
IMPROVEMENTS AND BUG FIXES
- update R requirement to (>= 3.5.0)
- processBismarkAln:
- add verbose argument
- update tests
- update docs
- joinsegmentneighbours:
- Catch case when only one groups is there
- regionCounts:
- update docs: mention that the output will be sorted by default
- Fixes #195
- vignette:
- add faq paragraph about regionCount to the vignette explaining
why we order input region
- update paragraph about methyldackel when to use
it instead of processBismarkAln
- Fixes #162
- add extensive test for bedgraph export
- update and export tests for getMethylationStats
- add extensive tests for getCoverageStats
- add extensive tests for normalizCoverage
- update checks for dataSim:
- if sample ids given check if length(sample.ids) == # replicates
- update tests for getMethylDiff
- unite destranding:
- make sure high numbers are not used in scientific notation
- fixes #129
- switch to data.table based destranding as it is faster and
more memory efficient for larger number of regions
- methseg:
- catch error when joined segments produce only single range
- Fixes #195
- calculateDiffmeth:
- check if output is equal for memory and tabix file
- Fixes #189
methylKit 1.15.2
IMPROVEMENTS AND BUG FIXES
- check.dbdir: catch if path equals root ("/") dir
- methRead:
- add missing context argument for call
to .procBismarkCytosineReport
- fixes https://github.com/al2na/methylKit/issues/198
methylKit 1.13.4
IMPROVEMENTS AND BUG FIXES
- set stringAsFactors to FALSE
- changed when reading data and tabix files
- this solves class missmatches downstream
- update methylKit data with stringsAsFactors off
- methRead:
- filter for given context when pipeline is cytosinereport
- order data when processing with methread, this ensures that
methylRaw and methylRawDB contain exact same data
- add additional test for methread, check whether methread
with or without tabix produces same data when processing
bismark coverage and cytosine report
- unite:
- make sure .CpG.dinuc.unifyOld equals .CpG.dinuc.unify
- add test to check that destranding result is same
for methylBase and methylBaseDB
methylKit 1.13.3
IMPROVEMENTS AND BUG FIXES
- getMethylDiff:
- fixes bugs in method for methylDiffDB
- suffix will be actual type now, was "type" before
- removed whitespaces in filename,
fixes https://github.com/al2na/methylKit/issues/171
- add extensive test for getmethylDiff function
- applyTbxByChunk:
- Allow optional writing of colnames and rownames if
returntype is text. Find details in
https://github.com/al2na/methylKit/issues/169
- percMethylation:
- return rownames for methylDB when rowids is TRUE,
fixes https://github.com/al2na/methylKit/issues/170
- add extensive tests for percMethylation
- reorganize:
- fix bug in method for methylBaseDB introduced with new tabix header
- add extensive testing for reorganize
- assocComp:
- add further checks for proper annotation
- removeComp:
- set default comp to NULL, to trigger earlier fail
- fix bug method for methylBaseDB introduced with new tabix header
- reconstruct:
- update checks for percent methylation matrix
- fix bug with fread
- add extensive tests for batch control functions
- diffMethPerChr:
- prevent from plotting when no chrom left
- add extensive tests for diffMethPerChr
methylKit 1.13.2
IMPROVEMENTS AND BUG FIXES
- fread.gzipped:
- add pre-checks wheter file exists and is not empty
- switch to R.utils::gunzip instead of building shell
command manually
- tileMethylCounts: remove orphan warning triggered by
incomplete temporary methylRaw object,
fixes https://github.com/al2na/methylKit/issues/175
- update vignette:
- add mincov argument to methread
- add paragraph to tiling section about reducing
coverage threshold + update example code
- update docs:
- rebuild docs with more recent version of roxygen
- exclude examples from internal function
- increase version requirement for tabix files with header
methylKit 1.13.1
IMPROVEMENTS AND BUG FIXES
- fix issues related to build checking:
- logical vectors of size longer than one
- docs for methseg contain line longer than 100 chars
- fix methSeg2bed error when seg.mean=0 and scores=NA by
replacing score with zero if average seg.mean is zero
https://github.com/al2na/methylKit/issues/123
- update vignette:
- explain how to get wig/bigwig file from methylKit
https://github.com/al2na/methylKit/issues/157
- explain how to deal with soft clipping in processBismarkAln
https://github.com/al2na/methylKit/issues/159
- add section about exporting and loading tabix objects
starting from version 1.13.1
methylKit 1.11.1
NEW FUNCTIONS AND FEATURES
- add functions to read and write a header to tabix files:
this allows for easier sharing of methylDB objects,
as the metadata is included in the tabix file
- new function readMethylDB: function reads the header from a given tabix file
and loads it into corresponding methylDB object
methylKit 1.9.4
NEW FUNCTIONS AND FEATURES
- calculateDiffMeth: introduce method "midPval" for fast testing of
different methylation if there is one sample per group,
contributed by @zellerivo
IMPROVEMENTS AND BUG FIXES
- calculateDiffMeth:
- fix rare case issue with invalid p-values on calculateDiffMeth call,
that caused "qvalue" p-value adjustment to fail
https://github.com/al2na/methylKit/issues/90
- let user choose between new "midPval" or older "fast.fisher" implemtation
for statistical test used to determine the methylation differences
https://github.com/al2na/methylKit/issues/96
- introduce p-value lookup table to reduce multiple testing of
identical configurations
https://github.com/al2na/methylKit/issues/96
- reduce code duplication and overhead by introducing S3 functions
to be called by S4 methods
- update vignette with section about usage of methylKit for analysis of
affinity- and array-based methylation assays
- methSeg: if object with multiple chromosomes is used, remove chroms with
less than two ranges
- unite: fix issue where digits were written in scientific notation
https://github.com/al2na/methylKit/issues/130
- getCorrelation: fix issue where getCorrelation produces matrix with NA
when using "min.per.group" https://github.com/al2na/methylKit/issues/137
methylKit 1.9.3
IMPROVEMENTS AND BUG FIXES
- getCorrelation: reduce code duplication and overhead by
introducing S3 functions to be called by S4 methods
- fread.gzipped: rewrite building of shell command with
system2 to mimic R.Utils::gunzip
- improve validity checks for methylDB objects
- pool: check length of treatment and number of sample is same
- headTabix: use fread.gzipped only when user wants to get more than 1e6 rows
- test-1-read: check if methylRawDB is same when directory is given or not,
i.e. test wether directory affects object
- methylRaw: check for content in tabix file, break if not
- calculateDiffMeth: dealing with case of full model not being different
from reduced model; print warning and set NaN to 1
- pool: check length of treatment and number of sample is same
- improve validity checks for methylDB objects
methylKit 1.9.2
IMPROVEMENTS AND BUG FIXES
- fread.gzipped: update function to check compression based on file content
and allow to decompress .bgz files
- headTabix: use fread.gzipped directly on the tabix file
fixes issue https://github.com/al2na/methylKit/issues/141
methylKit 1.9.1
IMPROVEMENTS AND BUG FIXES
- add methylRawListDB constructor
fixes https://github.com/al2na/methylKit/issues/134
- update validation functions for methylRaw/methylRawDB: check for single sample id
- unite: write S3 functions for class methylRawList and methylRawListDB
Fixes https://github.com/al2na/methylKit/issues/132
methylKit 1.7.10
IMPROVEMENTS AND BUG FIXES
- update man: update object and function descriptions to resolve
the 'file link treated as topic' warning under windows
methylKit 1.7.9
IMPROVEMENTS AND BUG FIXES
- bug fix: make internal function .checkdbdir more error proof
methylKit 1.7.8
IMPROVEMENTS AND BUG FIXES
- internal applyTbxByOverlap(): did not work correctly for return.type set to
"data.frame" or"data.table", due to missing argument.
https://github.com/al2na/methylKit/issues/131
methylKit 1.7.7
IMPROVEMENTS AND BUG FIXES
- unite(): skip checking if destranded tabix file exist
methylKit 1.7.6
NEW FUNCTIONS AND FEATURES
- methSeg(): introduce parameter 'initialize.on.subset' to subset data
for initialization of mixture modeling; update description; add tests
methylKit 1.7.4
IMPROVEMENTS AND BUG FIXES
- update link to test-file for methSeg() function
methylKit 1.7.3
IMPROVEMENTS AND BUG FIXES
- selectByOverlap(): update description; refine method signatures to
only support GRanges as range argument; update NAMESPACE to import
subjectHits() method from S4Vectors
methylKit 1.7.2
NEW FUNCTIONS AND FEATURES
- New constructor method methylRawList() can be used to combine
list of methylRaw objects into a methylRawList
IMPROVEMENTS AND BUG FIXES
- fix bug in methSeg: when joinSegments was activated,
diagnostic plot would always be plotted
- fixes in selectByOverlap() function: update description, to show that any
methylKit object (tabix or not) can be used with it ;
fixed broken method after @subjectHits was not available anymore
- fix error in .checkTabixFileExists function, that lead to overwriting of files
methylKit 1.5.3
IMPROVEMENTS AND BUG FIXES
- resolve absolute paths for dbdir argument
- initial check if output tabix file already exists and if yes rename output file
methylKit 1.5.2
IMPROVEMENTS AND BUG FIXES
- updated links to vignette and presentations in README
- fixed missspelling in show method of methylRawList object
- fixed getSampleID method for methylDiff object
- correct a not working code snippet in the vignette
methylKit 1.3.8
IMPROVEMENTS AND BUG FIXES
- changes to methCall(): more verbose output, reduce -Wunsigned warnings,
check for fragmented chromosome order, write conversion stats to extra file
- add Tests to check for chromosome disorder
methylKit 1.3.7
IMPROVEMENTS AND BUG FIXES
- if methylDiff object contains NA in a qvalue/meth.diff column
the getMethylDiff function returns an error. This is now fixed:
https://github.com/al2na/methylKit/issues/83
- Changed how the methylBase version of regionCounts handle missing values.
Before, a missing value made the whole region/tile missing. Now, a missing
value is treated as a site with zero coverage. Contributed by Karl Nordström:
https://github.com/al2na/methylKit/pull/77
methylKit 1.3.6
- changes to methSeg() function: update function description
by beeing more explicit about the sorting,
sort(x,ignore.strand=TRUE) is now called once if needed,
update tests
methylKit 1.3.5
IMPROVEMENTS AND BUG FIXES
- fix problem with methSeg() error occurring when GRanges is not sorted by position
methylKit 1.3.4
IMPROVEMENTS AND BUG FIXES
- fix problem with assocComp() on methylBaseDB
methylKit 1.3.3
IMPROVEMENTS AND BUG FIXES
- changes to calculateDiffMeth() function: add a message explaining
the calculation procedure based on either two or more treatment groups,
fixed bugs that prohibited the use of treatment groups other than 0/1
in two group case, allow for more than two groups, update tests
- changes in methSeg() function: update function documentation to
inform that provided Granges has to be sorted,
add check if granges is sorted and contains at least one meta.col
methylKit 1.3.2
IMPROVEMENTS AND BUG FIXES
- quick fix for long filename issue: in unite() and calculateMethylDiff()
instead of concatenated sample_ids, filename will be "methylBase"
concatenated with either 13-char random string or provided suffix
- updated vignette: added two short FAQs
methylKit 1.3.1
IMPROVEMENTS AND BUG FIXES
- fix conversion rate error in methCall()
methylKit 1.1.8
IMPROVEMENTS AND BUG FIXES
- fix methSeg error when only one segment is returned from fastseg,
add case handling for methSeg2bed
- check for user interruption in methCall to enable stop in execution
- changes to select() function: check for out-of-bound indices to
prevent downstream errors
methylKit 1.1.7
IMPROVEMENTS AND BUG FIXES
- fix methCall segementation fault, added tests and test files from bismark
- fixed missing p.value at coercion of methylBase to GRanges
- changes to the pool() function: save.db=TRUE for methylBaseDB by default,
differing lengths of given sample.ids and unique treatment lead to error,
added tests
- fix osx related error when reading gzipped files with methRead
- change deprecated function names in test files
- fixed bug with dataSim() function updated the manual
methylKit 1.1.6
IMPROVEMENTS AND BUG FIXES
- fixed a bug where tileMethylCounts() function did not work with
small chromosomes/scaffolds with few bases covered.
methylKit 1.1.5
IMPROVEMENTS AND BUG FIXES
- fixes missing error messages during methRead : https://github.com/al2na/methylKit/pull/57
methylKit 1.1.4
IMPROVEMENTS AND BUG FIXES
- merging tabix files is fixed: https://github.com/al2na/methylKit/pull/56
methylKit 1.1.3
IMPROVEMENTS AND BUG FIXES
- Typos in the vignette are fixed, thanks to Marcin Kosinski
methylKit 1.1.2
IMPROVEMENTS AND BUG FIXES
- Bug fixes in SAM file reading process. If there were more than one
header line there were problems in reading. Now this is fixed.
https://github.com/al2na/methylKit/pull/51
methylKit 1.1.1
IMPROVEMENTS AND BUG FIXES
- Fisher's exact test now works as described in the manual. It is automatically
applied in calculateDiffMeth() when there are only two groups with one
replicate each.
- During logistic regression modeling, the samples without counts are removed
from the model but the same filtering is not applied for covariates
data.frame, which can cause errors if min.per.group argument is used.
Now this is fixed: https://github.com/al2na/methylKit/issues/50
methylKit 0.99.4
IMPROVEMENTS AND BUG FIXES
- all annotation functions are now removed and are available
through genomation package. See the vignette for examples. Most
functions have similar names and functionality in genomation.
The users need to convert methylKit objects to GRanges using
as(methylKit.obj,"GRanges") before they can use genomation
functions.
methylKit 0.99.3
IMPROVEMENTS AND BUG FIXES
- Fixed a bug in processBismark() C++ function where BAM files are should be treated as 0-based.
Now this is fixed.
- Bug in calculateDiffMethDSS is fixed (https://github.com/al2na/methylKit/issues/49)
methylKit 0.99.2
IMPROVEMENTS AND BUG FIXES
- Fixed a bug in methRead() introduced after the addition of mincov argument.
the bug occurred only reading files legacy text files that have CpGs
with coverage below 10
- Changes to vignette for better description of the tests.
- Compiler error that occurs in older compilers are fixed via this PR
https://github.com/al2na/methylKit/pull/43
methylKit 0.99.1
IMPROVEMENTS AND BUG FIXES
- mostly changes to meet BioCcheck() requirements and reccomendations
- C++ code compiles on windows now, regex requirement is no longer there.
methylKit 0.9.6
IMPROVEMENTS AND BUG FIXES
- changes to following function names:
read() to methRead()
read.bismark to processBismarkAln()
adjust.methylC() to adjustMethylC()
get.methylDiff() to getMethylDiff()
annotate.WithFeature() to annotateWithFeature()
annotate.WithFeature.Flank() to annotateWithFeatureFlank()
annotate.WithGenicParts() to annotateWithGenicParts()
read.bed() to readBed()
read.feature.flank() to readFeatureFlank()
read.transcript.features() to readTranscriptFeatures()
- Improved documentation for methRead() (old read())
- Now, bismark cytosine report and coverage files can be read using methRead()
pipeline argument. see ?methRead
- Ported the Perl script for methylation base calling to C/C++ via Rcpp.
Contributed by Alexander Gosdschan.
- methRead() uses data.table::fread() to read files faster.
- methRead() has a new argument mincov, which sets the minimum number of
reads that needs to cover a base. Positions with coverage below this
number are discarded.
NEW FUNCTIONS AND FEATURES
- new function methSeg() can segment methylation (methylRaw objects) and
differential methylation (methylDiff objects) profiles to segments.
Associated function methSeg2bed() creates BED files from segments.
see ?methSeg. A test is added to check this in R CMD check.
Contributed by Arsene Wabo and Alexander Gosdschan.
- new tabix based classes methylRawDB, methylRawListDB, methylBaseDB,
methylDiffDB and respective methods implemented. Tests are updated to
check proper function in R CMD check. Contributed by Alexander Gosdschan.
- calculateDiffMeth() now supports basic overdispersion correction and multiple
methods for pvalue correction. The function also now handles covariates
such as age,sex etc. A test is added to check this in R CMD check.
Contributed by Adrian Bierling.
- New function calculateDiffMethDSS() is using beta-binomial model from DSS
package to calculate differential methylation. Contributed by
Dhruva Chandramohan with modifications from Altuna Akalin. This is a modified
version of the function from DSS package so that it can work with methylKit
objects.
- dataSim creates a methylBase object with simulated methylation data.
A test is added to check this in R CMD check. Contributed by Adrian Bierling.
methylKit 0.9.5
IMPROVEMENTS AND BUG FIXES
- travis CI build shield added
methylKit 0.9.4
IMPROVEMENTS AND BUG FIXES
- tileMethylCounts now works on methylBase objects, affected by BioC 3.0 upgrade.
A test is added to check this in R CMD check.
methylKit 0.9.3
IMPROVEMENTS AND BUG FIXES
- compatibility with BioC 3.0. Multiple BioC functions moved to other packages
within BioC,which broke some code and caused installation issues.
Now this is fixed.
- data.table::merge is now stable when all=TRUE. Removed my(altuna) version of data.table::merge
the code base.
methylKit 0.9.2.5
IMPROVEMENTS AND BUG FIXES
- calculateDiffMeth slim=FALSE argument works correctly when there are multiple
samples per group.
methylKit 0.9.2.4
IMPROVEMENTS AND BUG FIXES
- install_github() now works correctly. Removed blank lines at the end of
DESCRIPTION file.
- calculateDiffMeth and tileMethylCounts now works correctly,
typos were introduced in code with 0.9.2.2. Now these are fixed
methylKit 0.9.2.3
IMPROVEMENTS AND BUG FIXES
- regionCounts() bug occurring when the first argument is a class of methylBase is fixed.
The bug introduced an additional column to the resulting methylBase object.
https://groups.google.com/forum/#!topic/methylkit_discussion/p19K-pgavAI
methylKit 0.9.2.2
IMPROVEMENTS AND BUG FIXES
- unite() issues when destrand=FALSE is resolved. The issue appeared due to numeric vs.
integer conflict when merging data sets using chr,start and end locations.
- typo in calculateDiffMeth() argument "weighted.mean" is fixed.
- unite() is faster when destrand=TRUE, due to improvements in internal function
.CpG.dinuc.unify()
- regionCounts() strand.aware argument now works correctly. This bug had no effect
on tileMethylCounts. With the default arguments, strand aware setting was not
in effect at all, so every region was treated as strandless.
- Conversion to GRanges objects now removes seqlevels(chromosome names)
that are not used. Not removing these could cause problems in regionCounts()
function and functions depending on regionCounts().
- read() function in some cases was treating strand columns of the flat CpG
files as logical if strand had F or R letters and most of the first CpGs were
having F strand (Forward strand). Now this is fixed.
methylKit 0.9.2.1
IMPROVEMENTS AND BUG FIXES
- Fixes a bug in getMethylationStats() function that generates incorrect label numbers when the user overrides the default number
of breaks for the histogram. Contributed by Bonnie Barrilleaux.
methylKit 0.9.2
IMPROVEMENTS AND BUG FIXES
- A bug introduced with 0.9.1 is fixed. The bug occured when unite() function
is used with destrand=TRUE argument. It returned less number of CpGs then it was
supposed to, although returned CpGs had correct methylation and coverage values.
methylKit 0.9.1
NEW FUNCTIONS AND FEATURES
- objects takes less memory and they are reorganized. updateMethObject() updates
the objects from previous versions the latest version.
- New batch effect control functions are implemented. You can control if certain principal
components are associated with batch effects and remove those components from your
data. see ?assocComp amd ?removeComp. In addition, if you have corrected for the
batch effects via other methods, you can reconstruct a corrected methylBase object (
see ?reconstruct). Check the "batch effects" section in the vignette.
IMPROVEMENTS AND BUG FIXES
- unite() function takes less time due to use of data.table::merge
- fixes a bug appeared with R 3.02, where getting exon and intron coordinates
from BED12 files produced an error.
- tested with R 3.2 and matching bioconductor packages
- data(methylKit) has the new objects
methylKit 0.5.7
IMPROVEMENTS AND BUG FIXES
- tested with R 3.0 and matching bioconductor packages
- deprecated matchMatrix import from IRanges was causing a problem with package installation. v0.5.7 fixes that problem.
- Now there is no need for "chr" string in BED files when reading them as annotation files. Some assemblies do not have the "chr"" string in their chromosome names.
methylKit 0.5.6
NEW FUNCTIONS AND FEATURES
- new arguments for clusterSamples() and PCASamples() functions are added. With
the new options "sd.filter","sd.threshold","filterByQuantile" are added. These
options help finetune how low variation bases/regions are discarded prior to
clustering or PCA. See ?PCASamples and ?clusterSamples() for details on the
new options
- FAQ section added to the vignette
- show methods added for each class. Now, typing the variable name containing the
object will display concise information about the contents of the object.
- Subsetting objects via "[" notation is now enabled. You can subset rows of the
objects and it will return a new object rather than just a data frame.
IMPROVEMENTS AND BUG FIXES
- tileMethylCounts() error is fixed. Error occurred when tilling sparsely
covered small chromosomes like chrM in human RRBS data.
- read.bismark() can deal with Bismark output with Bowtie2. Bowtie2 can put gaps
in the alignment, now read.bismark() can deal with those gaps when parsing the
SAM file.
- Coverage columns are coerced to integer when reading generic methylation per
base files. BSMAP scripts can produce a methylation ratio file where coverages
(or "effective CT counts" as they are called) are not always integers, which
causes a problem in the downstream analysis. Now, these non-integer columns
are rounded to nearest integer while reading.
See http://zvfak.blogspot.com/2012/10/how-to-read-bsmap-methylation-ratio.html
for example usage of this functionality.
methylKit 0.5.5
IMPROVEMENTS AND BUG FIXES
- Differential methylation percentage calculation bug fixed. The bug occurred when "min.per.group" argument used in unite() function and when "weighted.mean=TRUE" in calculateDiffMeth() function.
- plotTargetAnnotation bug is fixed. Bug occured when "precedence" argument set to FALSE.
methylKit 0.5.4
IMPROVEMENTS AND BUG FIXES
- Examples added to help pages
- Changes to DESCRIPTION for complying with the bioconductor guidelines
- unused "cor" option removed from PCASamples() function
- some irrelevant functions are not exported (i.e they are not public) anymore.
- getContext() looks for the correct slot name now
methylKit 0.5.3
NEW FUNCTIONS AND FEATURES
- new function adjust.methylC() can be used to adjust measured 5mC levels by measured 5hmC levels
IMPROVEMENTS AND BUG FIXES
- pool() function bug fixed where one of the groups have one sample the pool function was not returning correct values
- calculateMethDiff() function option "SLIM" is now working. If set to TRUE SLIM method for q-value calculation will be used. If FALSE, p.adjust with method="BH" option will be used for P-value correction.
- read.bismark() function now works correctly under Windows.
- read.bismark() bug occurring when the reads are paired and overlapping is fixed now.
- read.bismark() bug occurring when the alignment is done in non-directional manner is fixed now. However, illumina sequencing protocols are directional and you are unlikely to have encountered this error if you aligned your sequences in a directional manner.
- getCorrelation() function has a new option called "method" can take the value of "spearman","person" or "kendall"
methylKit 0.5.2
NEW FUNCTIONS AND FEATURES
- new function pool() sums up coverage, numCs and numTs values within each group so one representative sample for each group will be created in a new methylBase object.
- new function normalizeCoverage() normalizes coverage and associated number of Cs and number of Ts values between samples using a scaling factor derived from the ratio between mean or median of coverage distributions of samples.
methylKit 0.5.1
IMPROVEMENTS AND BUG FIXES
- calculateDiffMeth() can now deal with differential methylation calculations where one group has multiple samples but the other one has only one.
methylKit 0.5
NEW FUNCTIONS AND FEATURES
- new function reorganize() can be used to reorganize methylRawList and methylBase objects to create new objects from subset of samples or can be used to change the order of samples and treatment vector.
- new function bedgraph() can output UCSC bedgraph files for methylRaw and methylDiff objects
- new function percMethylation() extracts percent methylation values from a methylBase object and returns a matrix
- unite() now can merge bases/regions that are not covered by all samples by setting "min.per.group" option
- PCASamples() has new options "transpose" and "sd.threshold". Now, one can do PCA analysis on the transposed % methylation values. "sd.threshold" is for removing rows with small variation prior to PCA analysis .see ?PCASamples for details
IMPROVEMENTS AND BUG FIXES
- regionCounts() bug that appeared with data.table 1.8.0 is fixed
- unite() bug that appeared with R 2.15 is fixed
- calculateDiffMeth() can deal with NA values introduced by setting "min.per.replicate" option of unite() function
- PCASamples() now uses "prcomp" function to do the PCA analysis
- external annotation data (cpgi.hg18.bed.txt and refseq.hg18.bed.txt) that comes with the package is now only a subset of full datasets. Do not use them for your own analysis, download the complete annotation data from UCSC or other sources in BED format.
methylKit 0.4.1
NEW FUNCTIONS AND FEATURES
- new function select() can be used to subset methylRaw, methylBase and methylDiff objects to create new objects with a subset of methylation data useful if you want to use only a particular portion of methylation events on the genome.
IMPROVEMENTS AND BUG FIXES
- read.bismark bug fixed, now it should be able to save methylation call files with no problem
methylKit 0.4
NEW FUNCTIONS AND FEATURES
- New read.bismark() function can read directly from a sorted SAM file output by Bismark aligner, the function can save methylation calls as text files or read them as methylRaw object to be used in analysis
- calculateDiffMeth() can do all differential methylation calculations using multiple-cores if 'num.cores' is set to an integer denoting how many cores should be used.
- getCoverageStats() & getMethylationStats() have a new option called 'labels', if set to FALSE, no labels will be drawn on top of the histogram bars.
IMPROVEMENTS AND BUG FIXES
- cov.bases option in tileMethylCounts() now works
- methylRaw,methylBase and methylDiff objects have a new slot 'resolution', which designates
whether methylation information is base-pair resolution or regional resolution. allowed values 'base' or 'region'
- getCoverageStats() & getMethylationStats() now print the sample ids and methylation context automatically in the
title when plotting
- getCoverageStats() & getMethylationStats() takes extra options to be passed to hist() function
- destrand option of unite() function will be over-ridden when methylRawList to be united contains regions rather than bases
- unite() function checks if supplied elements of methylRawList object have the same context,assembly and resolution before
uniting data sets.
- validity function checking the format of the data for a methylRaw object is implemented
- clusterSamples() and PCASamples() take methylation context information automatically and use it in plot titles
methylKit 0.3.1
IMPROVEMENTS AND BUG FIXES
- syntax error when fisher.test applied at calculateMethDiff() is fixed.