methstats: Exploratory statistics of samples in BSdataSet object
In kamalfartiyal84/methylPipe: Base resolution DNA methylation data analysis

Description Usage Arguments Details Value Author(s) Examples

Exploratory methylation statistics of samples in BSdataSet object.

1 2	## S4 method for signature 'methylPipe,BSdataSet' methstats(object, chrom, mcClass='mCG', minC=1, coverage=1, pval=1, Nproc=1)

`object`	An object of class BSdataSet
`chrom`	character; either NULL or an object of class character
`mcClass`	character; the mC sequence context to be considered, one of all, mCG, mCHG or mCHH
`minC`	numeric; the minumum number of reads with C (DNA-methylation events) at a given cytosine genomic position
`coverage`	numeric; the minimum number of total reads at a given cytosine genomic position
`pval`	numeric; the minimum binomial pValue for an mC call at a given cytosine genomic position
`Nproc`	numeric; the number of processors to use, one chromosome is ran for each processor

The function provides basic statistical methods which computes descriptive statistics, correlation matrix and clustering of samples within the BSdataSet.

A list with slots named descriptive_stats and correlation_mat.

Kamal Kishore

require(BSgenome.Hsapiens.UCSC.hg18)
uncov_GR <- GRanges('chr20', IRanges(14350, 18349))
H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)
IMR90data <- system.file('extdata', 'IMR90_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
IMR90.db <- BSdata(file=IMR90data, uncov=uncov_GR, org=Hsapiens)
H1.IMR90.set <- BSdataSet(org=Hsapiens, group=c("C","C","E","E"), IMR_1=IMR90.db, 
IMR_2=IMR90.db, H1_1=H1.db,H1_2=H1.db)
stats_res <- methstats(H1.IMR90.set,chrom="chr20",mcClass='mCG', Nproc=1)
stats_res