findQuads: Generate Reports on Potential G-quadruplex forming Strings...

In RyDe4/ChIPanalyzer: ChIPAnalyzer

Generate Reports on Potential G-quadruplex forming Strings near ChIP peaks using pqsfinder

Description

Searches for G-quadruplexes in DNA sequences around the ChIP peaks from the BED6 or greater file specified throught the function argument bedPath, and returns a list of reports for each sequence generated by the pqsfinder package.

Usage

findQuads(bedPath, seqWidth, assemblyVersion = "hg19")

Arguments

bedPath	the path to a BED6 or greater file containing processed ChIP-seq peaks. If data is not stranded, a period should be specified in the strand column.
seqWidth	the width of the sequence around the centre of each peak that should be searched for quadruplexes.
assemblyVersion	the genome assembly to retrive sequences from. Must be one of "hg19", "hg38", "mm9" or "mm10"

Value

returns a list of reports on potential quadruplex forming strings generated by pqsfinder::pqsfinder().

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

The Bioconductor Dev Team (2014). BSgenome.Hsapiens.UCSC.hg19: Full genome sequences for Homo sapiens (UCSC version hg19). R package version 1.4.0.

The Bioconductor Dev Team (2015). BSgenome.Hsapiens.UCSC.hg38: Full genome sequences for Homo sapiens (UCSC version hg38). R package version 1.4.1.

The Bioconductor Dev Team (2014). BSgenome.Mmusculus.UCSC.mm9: Full genome sequences for Mus musculus (UCSC version mm9). R package version 1.4.0.

The Bioconductor Dev Team (2014). BSgenome.Mmusculus.UCSC.mm10: Full genome sequences for Mus musculus (UCSC version mm10). R package version 1.4.0.

Lawrence M, Huber W, Pag\'es H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi:10.1371/journal.pcbi.1003118

H. Pagès, P. Aboyoun, R. Gentleman and S. DebRoy (2019). Biostrings: Efficient manipulation of biological strings. R package version 2.54.0.

Examples

path <- system.file("extdata", "MAZ_very_small_test.bed", package = "ChIPAnalyzer")
findQuads(bedPath = path, seqWidth = 200, assemblyVersion = "hg19")

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