sequenceCalc: Find occurences of a DNA pattern

In Repitools: Epigenomic tools

Description

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

Usage

  ## S4 method for signature 'GRanges,BSgenome'
sequenceCalc(x, organism, pattern, fixed = TRUE, positions = FALSE)
  ## S4 method for signature 'data.frame,BSgenome'
sequenceCalc(x, organism, window = NULL, positions = FALSE, ...)

Arguments

x	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

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.

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.

Author(s)

Aaron Statham

See Also

cpgDensityCalc, mappabilityCalc, gcContentCalc

Examples

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"))

Repitools documentation built on Nov. 8, 2020, 7:52 p.m.