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

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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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

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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.