matchPEM: find binding sites within some GenomicRanges or DNA sequences...

In zeropin/TFCookbook: Analyzing protein-DNA interactions data in principled way

find binding sites within some GenomicRanges or DNA sequences that match some PEM

Description

find binding sites within some GenomicRanges or DNA sequences that match some PEM

Usage

## S4 method for signature 'matrix,GenomicRanges'
matchPEM(PEM, subject, genome = GenomeInfoDb::genome(subject), E.cutoff = -3)

## S4 method for signature 'matrix,character'
matchPEM(PEM, subject, E.cutoff = -3)

## S4 method for signature 'matrix,DNAStringSet'
matchPEM(PEM, subject, E.cutoff = -3)

Arguments

PEM	a PEM matrix
subject	a list of DNA sequences
genome	the genome name, e.., hg38, mm10, etc
E.cutoff	the threshold to select hit

Methods (by class)

• matchPEM(PEM = matrix, subject = GenomicRanges): matrix/GenomicRanges

• matchPEM(PEM = matrix, subject = character): matrix/character

• matchPEM(PEM = matrix, subject = DNAStringSet): matrix/DNAStringSet

zeropin/TFCookbook documentation built on July 8, 2023, 2:59 p.m.