MotifAll: Analysis of motifs in protein sequences

Description Usage Arguments Value Author(s) Examples

View source: R/MotifAll.R

Description

This package implements the Motif_All algorithm

Usage

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MotifAll(x, idx_select, N_support = NULL, support = 0.05, signif = 0.05,
  var_p_val = "p_value_Z_score", k_min = 3, k_max = NULL,
  central_letter = NULL, match_central_letter = TRUE, showProgress = TRUE)

Arguments

x

a vector of sequences (with a fixed length). Defined as the background set

idx_select

Indexes of foreground sequences in x. Note that the foreground set must be a subset of the background set.

N_support

minimum support of motifs in the foreground set (number of counts). Has priority over support

support

minimum support of motifs in the foreground set (frequence)

signif

significance level of output motifs (p-value associated with the Z-score)

var_p_val

choose between p_value of Z-score ("p_value_Z_score")or p-value from hypergeometric test ("p_value_hyper")

k_min

minimum size of motifs

k_max

maximum size of motifs (set to NULL to ignore)

central_letter

search only for motifs that have the given character in central position

match_central_letter

Compute enrichment score on the restricted set of sequences that have the same central letter as the motif

showProgress

show progress bar in console

Value

A list including the following elements :

score : data frame with the motifs identified along with scores and counts

idx_match : list of vectors containing the matching indexes of a given motif in the set of sequences x

Author(s)

Guillaume Voisinne

Examples

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#load data :
dir<- system.file("extdata", package = "MotifAll")
path <- paste(dir, "/phospho_site_annotated_plus_motifs.txt", sep="")
df_motif <- read.csv(path, sep="\t")
#data(df_motif, package = "MotifAll")
psite <- "S"

idx_residue <- which(substr(as.character(df_motif$Sequence),8,8) == psite)
df <- df_motif[idx_residue, ]

x <- as.character(df$Sequence)
idx_select <- which(!is.na(df$Cluster))

res <- MotifAll(x, idx_select, support = 0.05, signif = 1e-4, k_min = 1, central_letter = psite)

VoisinneG/MotifAll documentation built on July 23, 2018, 4:13 a.m.