getReadDepth: getReadDepth

In chrisamiller/copyCat: Find regions of genomic copy number loss and gain from short reads

Description

Counts the number of sequence reads that fall into identically sized bins across the entire genome.

Usage

  getReadDepth(rdo)

Arguments

rdo	rdo: a readDepth Object, created with the command 'new("rdObject")'

Details

Assumes that the correct directory structure is in place (see full description in copyCat documentation)

In brief, the directory "reads" should be present and should contain read positions in bed format.

Value

returns the original rdObject with the @chrs attribute updated to contain a list of N data frames (one for each chromosome). Each data frame contains one column "rd" containing the counts for each bin.

Examples

  ##create a rdObject, set bin params
  # x <- new("rdObject")

  ##fill the bins with reads
  # x.reads <- getReadDepth(x)

chrisamiller/copyCat documentation built on July 20, 2021, 12:59 a.m.