sequenceCalc: Find occurences of a DNA pattern

Description

Function to find all occurrences of a DNA pattern in given locations.

Usage

"sequenceCalc"(x, organism, pattern, fixed = TRUE, positions = FALSE) "sequenceCalc"(x, organism, window = NULL, positions = FALSE, ...)

Arguments

A data.frame, with columns chr and position, or instead of the column position there can be columns start, end, and strand, or a GRanges object of the regions.

window

Bases around the locations supplied in x that are in the window. Calculation will consider windowSize/2-1 bases upstream, and windowSize/2 bases downstream.

organism

The BSgenome object to calculate CpG density upon.

pattern

The DNAString to search for.

fixed

Whether to allow degenerate matches.

positions

If TRUE FALSE

...

Arguments passed into the GRanges method

Value

If positions is TRUE, a list of vectors of positions of matches in relation to the elements of x, otherwise a vector of the number of matches for each element of x.

Details

If the version of the data frame with the start, end, and strand columns is given, the window will be created around the TSS.

Examples

Run this code

require(BSgenome.Hsapiens.UCSC.hg18)
TSSTable <- data.frame(chr=paste("chr",c(1,2),sep=""), position=c(100000,200000))
sequenceCalc(TSSTable, 600, organism=Hsapiens, pattern=DNAString("CG"))

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