getQuadCoveragePercentage: Get the percentage abundance of quadruplexes at positons...
In RyDe4/ChIPanalyzer: ChIPAnalyzer

getQuadCoveragePercentage

R Documentation

Get the percentage abundance of quadruplexes at positons across multiple sequences of equal length

Description

Using the matrix returned by getQuadMatrix, calculate the percentage abundance quadruplexes at positions dictated by the columns of quadMatrix

Usage

getQuadCoveragePercentage(quadMatrix)

Arguments

quadMatrix

a matrix in that format returned from getQuadMatrix, with each row representing a different sequence a columns representing positions, with a 1 indicated presence of a quadruplex and 0 otherwise

Value

a vector of percentages indicating the percentage of rows in quadmatrix that there was a 1(quadruplex) at the position represented by that column

Examples

path <- system.file("extdata", "MAZ_very_small_test.bed", package = "ChIPAnalyzer")
reports <- findQuads(bedPath = path,
 seqWidth = 200,
 assemblyVersion = "hg19")
qMatrix <- getQuadMatrix(quadReports = reports, maxOnly = TRUE)
quadCoveragePercentage <-
 getQuadCoveragePercentage(quadMatrix = qMatrix)

RyDe4/ChIPanalyzer documentation built on Sept. 1, 2023, 9:18 a.m.