methylPipe (version 1.6.2)

methstats: Exploratory statistics of samples in BSdataSet object

Description

Exploratory methylation statistics of samples in BSdataSet object.

Usage

## S3 method for class 'methylPipe,BSdataSet':
methstats(object, chrom, mcClass='mCG', minC=1, coverage=1, pval=1, Nproc=1)

Arguments

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

Value

• A list with slots named descriptive_stats and correlation_mat.

Details

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

Examples

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