readQSLIMFinderMain: Read and write QSLIMFinder results

In vitkl/SLIMFinderR: Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference

Description

Read and write QSLIMFinder results

Read and write QSLIMFinder results

Read and write QSLIMFinder results

Usage

readQSLIMFinderMain(outputfile = "forSLIMFinder_file_list$outputfile",
  check_exist = F)


  readQSLIMFinderOccurence(outputdir = "forSLIMFinder_file_list$outputdir",
  check_exist = F)

writePatternList(QSLIMFinder_main_result, filename = "./motifs.txt")

Arguments

outputfile	character vector of paths to QSLIMFinder main output files, one way to get these is writeInteractionSubsetFASTA_list()$outputfile
check_exist	if TRUE, check that each file exists / is not empty, if false - read all existing and non-empty files
outputdir	character vector of paths to QSLIMFinder output directories, one way to get these is writeInteractionSubsetFASTA_list()$outputdir
QSLIMFinder_main_result	data.table, the output of readQSLIMFinderMain()
filename	character, paths to file where to write motif list

Value

readQSLIMFinderMain: data.table combined from all QSLIMFinder main output files. Contains summary statistic on each motif found in each dataset

readQSLIMFinderOccurence: data.table combined from all QSLIMFinder occurence output files. Contains positions of motifs in each protein.

writePatternList: data.table containing Name and Pattern columns is saved as a tsv to filename, a format required for by comparimotif

Author(s)

Vitalii Kleshchevnikov

Vitalii Kleshchevnikov

Vitalii Kleshchevnikov

See Also

writeInteractionSubsetFASTA_list, runQSLIMFinder

vitkl/SLIMFinderR documentation built on May 3, 2019, 8:08 p.m.