GRangesINinteractionSubsetFASTA: Check if proteins in GRanges were used for motif search using...

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

Description

Check if proteins in GRanges were used for motif search using QSLIMFinder (SLIMFinder)

Usage

GRangesINinteractionSubsetFASTA(grange, interactionSubsetFASTA,
  query_only = F, clustermq = F)

Arguments

interactionSubsetFASTA	object of class InteractionSubsetFASTA_list containing: FASTA sequences for interacting proteins, molecular interaction data they correspond to. Each element of a list contains input for individual QSLIMFinder run.
query_only	return only GRanges for query proteins
GRanges	object containing instances of linear motifs or domains in proteins (identified by UniProtKB accession)

Value

list containing 2 vectors: which GRanges are in InteractionSubsetFASTA_list and seqlengths vector for these GRanges

Author(s)

Vitalii Kleshchevnikov

See Also

ELMdb2GRanges, runQSLIMFinder, SLIMFinderOcc2GRanges, listInteractionSubsetFASTA, randomGRanges

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