motif_cvp: Find consecutive but variable position (CVP) motif in a list...

In mengchen18/PTMotif: Detect PTM motifs

Description

Find consecutive but variable position (CVP) motif in a list of sequences

Usage

motif_cvp(seqs, min.seqs = 1, genes = NULL, ncores = 1)

Arguments

seqs	a character vector of sequences
min.seqs	minimum number of motif
genes	the gene name from where a sequences is discovered, a character vector has the same length as seqs
ncores	the number of cores to be used, passed to mclapply.

Value

a list consists of: $mw - motif wise count, a names integer vector. The names are the sequence motifs and the integers indicate the frequency of each motifs in the input sequences. $gw - gene wise count, a list of two elements: 1) unique gene and 2) motif genes, i.e. genes include a specific type of motif

Note

the algorithm uses an exhaustive approach to find all consecutive motifs, so it could be slow when the number of sequences is large.

Author(s)

Chen Meng

Examples

  seqs <- c(paste(LETTERS[1:6], collapse = ""),
  paste(LETTERS[2:7], collapse = ""),
  paste(LETTERS[3:8], collapse = ""),
  paste(LETTERS[4:9], collapse = ""),
  paste(LETTERS[5:10], collapse = ""))
  motif_cvp(seqs)

mengchen18/PTMotif documentation built on May 29, 2019, 6:53 p.m.