motif.count: Low level function to detect motifs in strings

In HajkD/LTRpred: De novo functional annotation of retrotransposons

Low level function to detect motifs in strings

Description

Find a specific motif or a sequence of motifs within genomic sequences.

Usage

motif.count(seq.file, motif, as.ratio = FALSE)

Arguments

seq.file	path to the genomic sequecne file of interest (e.g. LTR TE seqs predicted by LTRpred).
motif	a character string or vector of strings which shall be counted within each sequence.
as.ratio	shall count values be returned as asbolute frequency (count value) or as relative frequency (percentage).

Author(s)

Hajk-Georg Drost

Examples

# find number of "CG" motifs in predicted LTR transposons
motif.count(seq.file = system.file("LTRseqs.fas",package = "LTRpred"), 
            motif    = "CG")
            
# find number of "CG" motifs in predicted LTR transposons: rel. frequency
motif.count(seq.file = system.file("LTRseqs.fas",package = "LTRpred"), 
            motif    = "CG",
            as.ratio = TRUE)             

HajkD/LTRpred documentation built on April 22, 2022, 4:35 p.m.