get_motifs_list: Motif enrichment using rmotifx.

In ecnuzdd/PhosMap: A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

Motif enrichment using rmotifx.

Description

Motif enrichment using rmotifx.

Usage

get_motifs_list(foreground, background, center_vector, motifx_pvalue)

Arguments

foreground	A vector for aligned sequences as the foreground input.
background	A vector for aligned sequences as the background input.
center_vector	A vector for aligned centers.
motifx_pvalue	A numeric value for selecting motifs that meets the minimum cutoff.

Value

A list for results of motif enrichment.

Author(s)

Dongdong Zhan and Mengsha Tong

References

Omar Wagih (2014). rmotifx: An iterative statistical approach to the discovery of biological sequence motifs. R package version 1.0.

Examples

## The process needs to load data from PhosMap datasets stored into FTP server and perform large computation.
## It may take a few minutes.
if(FALSE){
    ftp_url <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/get_motifs_list.RData"
    load_data <- load_data_with_ftp(ftp_url, 'RData')
    writeBin(load_data, "get_motifs_list.RData")
    load("get_motifs_list.RData")

    motifs_list <- get_motifs_list(foreground[1:100], background[1:100], center_vector, motifx_pvalue)
    head(motifs_list)
}

ecnuzdd/PhosMap documentation built on Dec. 7, 2022, 4:09 a.m.