NEWS

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methylPipe 1.17.1

• updated or fixed the following functions: + getCposDensity : fixed the warning message in checking for NA in a list

methylPipe 1.4.3

• updated or fixed the following functions: + findDMR: updated the function to allow it to run without number of processor specification

methylPipe 1.4.2

• updated or fixed the following functions: + meth.stats: updated the coverage object error in this function

methylPipe 1.4.1

• updated or fixed the following functions: + pool.reads: added this new function to pool reads of replicates into a single file for each condition

methylPipe 1.3.3

• updated or fixed the following functions: + profileDNAmetBinParallel: fixed the error when there is single minus strand in GRanges for profiling

methylPipe 1.3.2

• updated or fixed the following functions: + meth.call: coverage is outputted now as an GRanges object + findDMR: coverage threshold is used even for unmethylated cytosines + getCposChr: fixed bug which was ignoring Cytosines at the boundary of genomic ranges on both sides

methylPipe 1.2.1

• updated or fixed the following functions: + plotMeth: updated arguments: grl, brmeth and genomic co-ordinates; removed arguments: Datatrackname + updated vignette

methylPipe 1.0.4

• updated or fixed the following functions: + BSprepare: fixed the problem of chromosome name with numeric values + updated all examples with updated tabix indexed files + updated vignette

methylPipe 1.0.3

• updated or fixed the following functions: + BSprepare: fixed the problem of unsorted files + BSprepare: fixed the problem of methylation files with numeric chromosome name + methstats: Added a new function to provide descriptive statistics of methylation data

methylPipe 1.0.2

• updated or fixed the following functions: + profileDNAmetBinParallel + updated R version dependency information

methylPipe 1.0.0

• initial version with the following functions implemented: + mCsmoothing + findPMDs + plotAnnoBar + mapBSdata2GRanges + findDMR + consolidateDMRs + getCpos + profileDNAmetBin + plotMeth + BSprepare + meth.call + GElist-class + GEcollection-class + BSdataSet-class + BSdata-class