gcContentCalc: Calculate The gcContent of a Region

In markrobinsonuzh/Repitools: Epigenomic tools

Calculate The gcContent of a Region

Description

Function to calculate the GC content of windows

Usage

  ## S4 method for signature 'GRanges,BSgenome'
gcContentCalc(x, organism, verbose = TRUE)
  ## S4 method for signature 'data.frame,BSgenome'
gcContentCalc(x, organism, window = NULL, ...)

Arguments

x	A GRanges object or a data.frame, with columns chr and either position or start, end and strand.
window	Bases around the locations that are in the window. Calculation will consider windowSize/2 bases upstream, and windowSize / 2 - 1 bases downstream.
organism	The BSgenome object to calculate gcContent upon.
verbose	Whether to print the progess of processing.
...	The verbose variable for the data.frame method, passed onto the GRanges method.

Details

The windows considered will be windowSize/2 bases upstream and windowSize/2-1 bases downstream of the given position, for each position. The value returned for each region is a percentage of bases in that region that are a G or C.

Value

A vector of GC content percentages, one for each region.

Author(s)

Aaron Statham

Examples

require(BSgenome.Hsapiens.UCSC.hg18)
TSSTable <- data.frame(chr = paste("chr", c(1,2), sep = ""), position = c(100000, 200000))
gcContentCalc(TSSTable, 200, organism=Hsapiens)

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.