RnBeads (version 1.4.0)

get.cpg.stats: get.cpg.stats

Description

Computes CpG-related statistics for the specified regions.

Usage

get.cpg.stats(chrom.sequence, starts, ends)

Arguments

chrom.sequence

Chromosome sequence, usually obtained from the assembly's genome definition. This must be an object of type MaskedDNAString.

starts

integer vector of start positions for the regions of interest.

ends

integer vector of end positions for the regions of interest.

Value

Table of statistics for the regions in the form of a matrix with the following columns: "CpG" and "GC". The columns contain the number of CpG dinucleoties and the number of C and G bases in each region.