MotifAll: Analysis of motifs in protein sequences
In VoisinneG/MotifAll: Analysis of motifs in protein sequences

Description Usage Arguments Value Author(s) Examples

This package implements the Motif_All algorithm

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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)

`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

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

Guillaume Voisinne

#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)