NEWS

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mosaics 2.9.9

BUG FIXES

• generateWig(): fix the error specific to the BAM file format, which generated unnecessary lines in the output WIG file.

mosaics 2.9.8

BUG FIXES

• construtBins(), generateWig(), extractReads(): 'readGAlignments' replaces the defunct 'readGAlignmentsFromBam'.
• extractReads(), findSummit(), adjustBoundary(), filterPeak(): more safeguards added.
• constructBins(): fix typo.

mosaics 2.9.7

BUG FIXES

• mosaicsPeak(): fix the error that chrID is missing.
• adjustBoundary(): fix the error that chrID is incorrectly processed.
• constructBins(), generateWig(), extractReads(): fix the error for the processing of BAM files for PET data.

mosaics 2.9.6

SIGNIFICANT USER-VISIBLE CHANGES

• export(): aveLogP is report as column 9 for 'narrowPeak' and 'broadPeak' file formats.

mosaics 2.9.5

SIGNIFICANT USER-VISIBLE CHANGES

• extractReads(): Users can now choose whether to keep read-level data with the argument 'keepReads'.
• Object sizes are significantly decreased for the output of extractReads(), findSummit(), adjustBoundary(), and filterPeak().
• MosaicsPeak class definition is modified to reflect the changes above.
• In the peak lists, now, logMinP and logAveP (i.e., -log10 transformation of minP and aveP, respectively) are reported instead of minP and aveP, respectively.
• show() method becomes significantly faster.

mosaics 2.9.4

SIGNIFICANT USER-VISIBLE CHANGES

• Peak list now incorporates mean(-log10(PP)), summitSignal, and summit.
• In the peak list, the counts of control samples and the log ratio of ChIP over control counts are adjusted by the ratio of sequencing depth, instead of the ratio of sum of ChIP and control counts.
• postProb(): Return posterior probabilities for arbitrary peak regions.
• export() becomes significantly faster.
• construtBins(): calculate sequencing depth and keep this information in the first line (commented) of bin-level files.
• seqDepth(): returns sequencing depth information, which can be applied to all of BinData, MosaicsFit, MosaicsHMM, MosaicsPeak class objects.
• Name of method coverage() is changed to readCoverage().

BUG FIXES

• findSummit() & adjustBoundary(): fix the error that an average point of multiple apart summit ties is reported as a summit. Now, the first summit block is chosen first and then an average point of the first summit block is reported as a summit. Also, fix some minor numerical issues regarding the calculation of summit locations.
• filterPeak(): fix the error that the improvement of ChIP over control samples is set to zero when there is no control signal at the position. Now, in this case, control signal is set to zero.
• adjustBoundary(): fix the error "multiple methods tables found for ‘coverage’" in R CMD check.

mosaics 2.9.3

SIGNIFICANT USER-VISIBLE CHANGES

• The vignette and the help documents are updated and polished.

BUG FIXES

• generateWig(): fix the error that values in the exported files are written in scientific notation.
• constructBins(): fix the error that values in the exported files are written in scientific notation.

mosaics 2.9.2

BUG FIXES

• extractReads(): fix the error that strands are incorrectly handle when loading read-level data.
• export(): fix the error to incorrectly ask to run exportReads() when it is not needed.

mosaics 2.9.1

SIGNIFICANT USER-VISIBLE CHANGES

• The vignette and the help documents are updated and polished.

BUG FIXES

• adjustBoundary(): fix the error that boundaries are incorrectly adjusted.

mosaics 2.9.0

SIGNIFICANT USER-VISIBLE CHANGES

• extractReads(): Load read-level data and extract reads corresponding to each peak region.
• findSummit(): Find a summit within each peak, based on local ChIP profile.
• adjustBoundary(): Adjust peak boundaries (designed for histone modification peaks).
• filterPeak(): Filter peaks based on their peak lengths and signal strengths.
• mosaicsPeakHMM: Posterior decoding is set to default (decoding="posterior").
• mosaics package now additionally depends on GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, and S4Vectors packages.

BUG FIXES

• export(): fix the error that values in the exported files are written in scientific notation.

mosaics 2.0.2

BUG FIXES

• generateWig(): fix final coordinates when useChrfile=TRUE and chrfile is provided (not affect PET data).

mosaics 2.0.1

BUG FIXES

• constructBins() & generateWig(): the new error in version 2.0.0 fixed.

mosaics 2.0.0

• BioConductor release 3.0.

mosaics 1.99.4

SIGNIFICANT USER-VISIBLE CHANGES

• Typos in the vignette are fixed.

mosaics 1.99.3

BUG FIXES

• mosaicsFit(): mismatch between function and help fixed.

mosaics 1.99.2

SIGNIFICANT USER-VISIBLE CHANGES

• mosaicsFit(): Sets bgEst="rMOM" as default.
• Help documents are polished and updated.
• Vignette is updated.

mosaics 1.99.1

SIGNIFICANT USER-VISIBLE CHANGES

• mosaicsFitHMM() & mosaicsPeakHMM(): Hidden-Markov-Model-based MOSAiCS model fitting & peak calling, respectively, to identify broad peaks such as histone modifications.
• Add new class 'MosaicsHMM' with methods show(), plot(), & estimates().
• mosaicsFit(): Introduces a new argument 'trans'.
• mosaicsFit(): Stability & robustness of model fitting were improved.
• Polish help documents of constructBins(), generateWig(), and mosaicsRunAll().
• Tested to work with >= R 3.0 properly.

BUG FIXES

• constructBins() & export(): Use correct base for BED file (one base shift).
• Reflect the changes in Rcpp packages that mosaics package depends on.

mosaics 1.5.3

BUG FIXES

• mosaicsRunAll(): Bug fix when byChr = TRUE.

mosaics 1.5.2

SIGNIFICANT USER-VISIBLE CHANGES

• constructBins(): Supports aligned read file formats for PET data (eland results and SAM formats).
• mosaicsRunAll(): Supports aligned read file formats for PET data.
• Add generateWig(): Constructs wiggle files for PET and SET data.
• Use tab separator instead of whitespaces for generateWig() and constructBins().
• Improve the vignette (case studies, example lines for input files, generateWig()).

BUG FIXES

• constructBins(): Bug fix for capping and excludeChr. Fix incorrect summary when byChr = TRUE.
• mosaicsRunAll(): Bug fix for excludeChr & handling the full path for chipFile and controlFile.

mosaics 1.5.1

SIGNIFICANT USER-VISIBLE CHANGES

• constructBins(): Chromosome information can now be specified.
• mosaicsRunAll(): Chromosome information can now be specified.

mosaics 1.4.1

BUG FIXES

• constructBins(): Bug fix for the "outfileLoc" argument.
• mosaicsFit(): Minor changes in two-signal-component model fitting.
• mosaicsPeak(): No warning with the updated IRanges package.

mosaics 1.4.0

• BioConductor release 2.10.

mosaics 1.3.4

SIGNIFICANT USER-VISIBLE CHANGES

• Improve help documents for all classes and functions.

BUG FIXES

• mosaicsPeak(): Correct bin size calculation when binsize=NA.

mosaics 1.3.2

SIGNIFICANT USER-VISIBLE CHANGES

• Simplify arguments of mosaicsRunAll(), constructBind(), and export().
• Add parallel argument in mosaicsFit().
• Extensive use of parallel processing/computing.
• Overall speed improvements in the package.
• Update the vignette.
• Use parallel package instead of multicore package.

mosaics 1.2.5

• Correct version number in DESCRIPTION and package?mosaics.

mosaics 1.2.4

SIGNIFICANT USER-VISIBLE CHANGES

• Add parallel argument in readBins().
• Add parallel argument in mosaicsRunAll().

BUG FIXES

• DESCRIPTION: 'multicore' package in 'Enhances' instead of 'Suggests'.

mosaics 1.2.3

NEW FEATURES

• New model for deeply sequenced ChIP-seq data.
• Genome-wide analysis of ChIP-seq data is now available.
• Supports more aligned read file formats: eland_result, eland_extended, eland_export, bowtie, SAM, BED, CSEM.
• Preprocessing of aligned read files can be done within the R environment using constructBins().
• Easier model fitting for the two sample analysis using mosaicsRunAll().
• Preprocessing and model fitting become much faster (Rcpp).
• Parallel processing/computing is now supported (multicore).

SIGNIFICANT USER-VISIBLE CHANGES

• Add constructBins(): Preprocess aligned read files to bin-level files.
• Add mosaicsRunAll(): Convenient two sample analysis.
• Add bgEst argument in mosaicsFit(): Choose background estimation approach.
• Add nCore argument in readBins(): Parallel processing.
• Vignettes is now extensively updated.
• Rcpp package is required and multicore package is suggested.

DEPRECATED AND DEFUNCT

• Drop chrID argument in export().

BUG FIXES

• Fix mosaicsPeak() for the case that no peak is called.
• Fix export() by removing unnecessary spaces in output text files.

mosaics 1.2.0

• BioConductor release 2.9.

mosaics 1.0.1

• Fixes for 'plot' method of class 'binData'.

mosaics 1.0.0

• On BioConductor (release 2.8).