mea_based_on_background: Motif enrichment based on global background (fasta library...

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

Motif enrichment based on global background (fasta library from Refseq).

Description

Motif enrichment based on global background (fasta library from Refseq).

Usage

mea_based_on_background(foreground, AA_in_protein, background, motifx_pvalue)

Arguments

foreground	A vector for aligned sequence of foreground.
AA_in_protein	A vector for the location of S/T/Y in sequence of protein.
background	A vector for aligned sequence of background.
motifx_pvalue	A numeric value for selecting motifs that meets the minimum cutoff.

Value

A list containing motifs and the corresponding sequences

Author(s)

Dongdong Zhan and Mengsha Tong

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/mea_based_on_background.RData"
    load_data <- load_data_with_ftp(ftp_url, 'RData')
    writeBin(load_data, "mea_based_on_background.RData")
    load("mea_based_on_background.RData")

    motifs_list <- mea_based_on_background(
      foreground[1:100],
      AA_in_protein[1:100],
      background[1:1000],
      motifx_pvalue
    )
}

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