seach_motif_pattern: Convert data frame of motif to the sequence pattern

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

Convert data frame of motif to the sequence pattern

Description

Convert data frame of motif to the sequence pattern

Usage

seach_motif_pattern(
  foreground_sequence,
  background_sequence,
  min_sequence_count = 1,
  min_pvalue = 0.01,
  center = "S",
  width
)

Arguments

foreground_sequence	A vector for AA sequences with fixed length as foreground input.
background_sequence	A vector for AA sequences with fixed length as background input.
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.
center	A character for center of k-mer.
width	A numeric for specific k-mer.

Value

A list for information summary of searching mortif

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

motif_result_loop_i <- seach_motif_pattern(
  loop_foreground[1:100],
  loop_background[1:1000],
  min_sequence_count = min_sequence_count,
  min_pvalue = min_pvalue,
  center = center,
  width = check_result_list$width
)
head(motif_result_loop_i)

}

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