listSingleInteractFromSet2: Split interaction subset from 2 sets so that each elements...

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

Description

Split interaction subset from 2 sets so that each elements contains only one of the proteins from set 2, and retrieve FASTA sequences for each

Usage

listSingleInteractFromSet2(subset1, single_interact_from_set2, set1_only,
  fasta)

Arguments

subset1	interaction_subset_from_2_sets object produced by subset2setsBy1ID
single_interact_from_set2	logical, split sequence sets to contain only one protein from interaction_set2 (only one query protein for QSLIMFinder). If FALSE, set2 will contain all proteins that interact with an element of seed_id_vect (which means multiple query proteins for QSLIMFinder).
set1_only	logical, only relevant if single_interact_from_set2 = TRUE, sequence set1 should contain only proteins that interact with an element of seed_id_vect in interaction_set1. If FALSE, proteins that interact with an element of seed_id_vect in interaction_set2 with the exception of the single one () are also included. Argument for singleInteractFromSet2
fasta	list containing AAStringSet renamed by recodeFASTA and mapping table from recodeFASTA

Value

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.

Author(s)

Vitalii Kleshchevnikov

See Also

subset2setsBy1ID, listInteractionSubsetFASTA

Examples

subset1_fasta = listSingleInteractFromSet2(subset1, single_interact_from_set2, set1_only, fasta)

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