get_motif_analysis_summary: Get summary results of motif analysis for specific input

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

Get summary results of motif analysis for specific input

Description

Get summary results of motif analysis for specific input

Usage

get_motif_analysis_summary(
  foreground,
  background,
  center = "S",
  min_sequence_count = 1,
  min_pvalue = 0.01
)

Arguments

foreground	A vector for AA sequences with fixed length as foreground input.
background	A vector for AA sequences with fixed length as background input.
center	A character for center of k-mer.
min_sequence_count	A numeric for the minimum sequence number assigned to a motif.
min_pvalue	A numeric for the minimum pvalue for found motif.

Value

A list for summary result of motif analysis

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_motif_analysis_summary.RData"
    load_data <- load_data_with_ftp(ftp_url, 'RData')
    writeBin(load_data, "get_motif_analysis_summary.RData")
    load("get_motif_analysis_summary.RData")

    motifs <- get_motif_analysis_summary(
      foreground[1:100], background[1:100],
      center = center,
      min_sequence_count = 1,
      min_pvalue = motifx_pvalue
    )
    head(motifs)
}

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