gcContentCalc: Calculate The gcContent of a Region
In Repitools: Epigenomic tools

Description Usage Arguments Details Value Author(s) Examples

Function to calculate the GC content of windows

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

`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.

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.

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

Aaron Statham

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