Description Usage Arguments Value Author(s) Examples
This package implements the Motif_All algorithm
1 2 3 |
x |
a vector of sequences (with a fixed length). Defined as the background set |
idx_select |
Indexes of foreground sequences in |
N_support |
minimum support of motifs in the foreground set (number of counts).
Has priority over |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | #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)
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