getQuadMatrix: Get A Matrix Representing the positions of G-quadruplexes in...

In RyDe4/ChIPanalyzer: ChIPAnalyzer

Get A Matrix Representing the positions of G-quadruplexes in Multiple Sequences

Description

Create a matrix with a number of rows equivalent to the number of reports in quadReports, and a number of columns equal to seqWidth, where each entry is 1 iff there is a quadruplex at that position in the sequence for the report for that row, and a 0 otherwise.

Usage

getQuadMatrix(quadReports, maxOnly = TRUE)

Arguments

quadReports	a list of reports (type PQSviews) generated by pqsfinder in the function findQuads. The length of the sequences reported on must be the same and equal to seqWidth
maxOnly	if TRUE, only the maximum scoring G-quadruplexes for each sequence are used.

Value

a matrix with dimensions length(quadReports) X seqWidth

References

Hon J, Martinek T, Zendulka J, Lexa M. (2017) pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics. 33(21), 3373-3379. https://doi.org/10.1093/bioinformatics/btx413

Examples

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

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