getStats: Obtain statistics from a BSseqTstat object

In hansenlab/bsseq: Analyze, manage and store whole-genome methylation data

Obtain statistics from a BSseqTstat object

Description

Essentially an accessor function for the statistics of a BSseqTstat object.

Usage

getStats(bstat, regions = NULL, ...)

Arguments

bstat	An object of class BSseqStat or BSseqTstat.
regions	An optional data.frame or GenomicRanges object specifying a number of genomic regions.
...	Additional arguments passed to the different backends based on the class of bstat; see Details.

Details

Additional argument when the bstat object is of class BSseqTstat:

stat

Which statistics column should be obtained.

Value

An object of class data.frame possible restricted to the regions specified.

Author(s)

Kasper Daniel Hansen [e-mail]

See Also

BSseqTstat for the BSseqTstat class, and getCoverage and getMeth for similar functions, operating on objects of class BSseq.

Examples

if(require(bsseqData)) {
  data(BS.cancer.ex.tstat)
  head(getStats(BS.cancer.ex.tstat))
  reg <- GRanges(seqnames = c("chr22", "chr22"),
     ranges = IRanges(start = c(1, 2*10^7), end = c(2*10^7 +1, 4*10^7)))
  head(getStats(BS.cancer.ex.tstat, regions = reg))
}

hansenlab/bsseq documentation built on Nov. 6, 2024, 2:59 p.m.