jg.getControlCounts: jg.getControlCounts

In andrewholding/Brundle: Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data

Description

This function counts the number of aligned reads in millions from a list of bam files. It returns these in as a list of numbers in the same order.

Usage

jg.getControlCounts(jg.control, jg.controlSampleSheet, jg.Condition)

Arguments

jg.control	is a peakset extracted by jg.dbaGetPeakset.
jg.controlSampleSheet	is the samplesheet supplied to DiffBind to generate jg.control.
jg.Condition	is the condition we the counts for as specficied in the samplesheet.

Examples

data(jg.controlPeakset, package="Brundle")
fpath <- system.file("extdata", "samplesheet_SLX14438_hs_CTCF_DBA.csv",package="Brundle")
jg.controlSampleSheet<-fpath
jg.controlCountsTreated<-jg.getControlCounts(jg.controlPeakset, jg.controlSampleSheet,"Fulvestrant")

andrewholding/Brundle documentation built on May 10, 2019, 5:17 a.m.