runCompariMotif3: Run CompariMotif3

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

Description

Run CompariMotif3

Usage

runCompariMotif3(input_file = "./SLIMFinder/result/motifs.txt",
  slimpath = "../software/slimsuite/tools/", dbpath = "./data_files/",
  dburl = "http://elm.eu.org/elms/elms_index.tsv",
  parameters = "unmatched=T motific=T",
  out_file = "./SLIMFinder/result/comparimotif.tdt",
  LSF_project_path = "/hps/nobackup/research/petsalaki/users/vitalii/vitalii/viral_project/",
  run = F, with = c("self", "db")[2])

Arguments

input_file	a path to a tsv file containing Name and Pattern columns
slimpath	path to /slimsuite/tools/
dbpath	path to directory where to save and keep ELM database (http://elm.eu.org/) or other database of linear motifs in a format required by comparimotif_V3: http://rest.slimsuite.unsw.edu.au/docs&page=module:comparimotif_V3
dburl	url where to download database
parameters	any commandline parameters for comparimotif_V3 as a single character string
out_file	path to a file where comparimotif_V3 should save the result
LSF_project_path	path to the project directory on the LSF cluster file system. If on LSF is to be used all other paths should be relative to this directory, alternatively, set this argument to empty character. Final path is LSF_project_path concatenated with input_file, slimpath, out_file or dbpath. When using this on a local machine set this argument to empty character.
run	logical, run comparimotif_V3 (T) or just output the command (F), can be useful for check correcteness
with	compare motifs in input_file to the database in dbpath ("db") or to input_file ("self")

Value

system command to be run or that was run

Author(s)

Vitalii Kleshchevnikov

See Also

writeInteractionSubsetFASTA_list, runQSLIMFinder

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