listInteractionSubsetFASTA: get FASTA sequences of proteins that interact with seed...

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

Description

get FASTA sequences of proteins that interact with seed proteins (datasets for QSLIMFinder)

Usage

listInteractionSubsetFASTA(interaction_set1, interaction_set2,
  seed_id_vect, fasta, single_interact_from_set2 = T, set1_only = T)

Arguments

interaction_set1	cleanMItab object containing molecular interactions (such as all interactions between human proteins)
interaction_set2	a different cleanMItab object containing molecular interactions (conceptually different source of interaction data, such as other type of interactions or human-viral interactions)
seed_id_vect	a vector of interactor IDs for which to retrieve interactions (for each separately)
fasta	AAStringSet containing sequences for all proteins in interaction_set1 and interaction_set2
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 but are not a single query protein are also included. Argument for singleInteractFromSet2

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, recodeFASTA, interactionSubsetMapID, recodeANDinteractionSubsetFASTA, singleInteractFromSet2, listSingleInteractFromSet2, filterInteractionSubsetFASTA_list

Examples

forSLIMFinder = listInteractionSubsetFASTA(interaction_set1 = all_human_interaction,
                 interaction_set2 = all_viral_interaction,
                 seed_id_vect = proteins_w_signif_domains,
                 fasta = all.fasta,
                 single_interact_from_set2 = T, set1_only = T)

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