methstats {methylPipe} | R Documentation |
Exploratory methylation statistics of samples in BSdataSet object.
## 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