printMotifDomainTable: 'printMotifDomainTable' combines Domain enrichment and Motif...

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

Description

printMotifDomainTable combines Domain enrichment and Motif search results

Usage

printMotifDomainTable(input, doman_viral_pairs = F, motifs = F,
  destfile, fdr_pval_thresh = 0.05, only_with_motifs = F,
  fdr_motifs = 1, occurence_QSLIMFinder = NA, comparimotif_wdb = NA,
  patterns_QSLIMFinder = NA, print_table = T, one_from_cloud = T,
  entry.list = NULL)

Arguments

input	object of class XYZinteration_XZEmpiricalPval and should be the output of permutationPval()
doman_viral_pairs	if TRUE - remove human proteins to have a row per viral protein - human domain pair, if FALSE a row is per viral protein - human domain - human protein.
motifs	add motif search results?
destfile	file where to save the resulting table
fdr_pval_thresh	FDR threshold p-value for Domain enrichment analysis
only_with_motifs	show enriched domains only if motif in viral proteins are also present (if FALSE - show all results)
fdr_motifs	FDR threshold p-value for Motif search analysis
occurence_QSLIMFinder	data.table containing the motif occurence output of the QSLIMFinder
comparimotif_wdb	data.table containing the output of the comparimotif tool (comparing motifs from occurence_QSLIMFinder to ELM DB)
print_table	if TRUE calls DT:datatable to print the interactive results table
one_from_cloud	pick only one motif per motif cloud by the lowest p-value (before multiple hypothesis testing correction)

Author(s)

Vitalii Kleshchevnikov

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