domainProteinPairMatch: Check if the protein in the set2 is associated with domain...

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

Description

Check if the protein in the set2 is associated with domain that is contained in the protein in the name and remove if not

Usage

domainProteinPairMatch(InteractionSubsetFASTA_list, domain_res,
  non_query_domain_res = NULL, non_query_domains_N = 0,
  non_query_set_only = T, query_domains_only = F, remove = T)

Arguments

InteractionSubsetFASTA_list	object of class InteractionSubsetFASTA_list created by listInteractionSubsetFASTA
domain_res	the result of domain enrichment analysis: object class XYZinteration_XZEmpiricalPval, the output of permutationPval. The domain should be in nodeZ, the set2 protein should be in the nodeX, the set1 protein should be in the nodeY.
non_query_domain_res	the result of domain enrichment analysis for non-query proteins, when provided will be used for filtering.
non_query_domains_N	the number of non-query proteins with predicted domains for each dataset. Used only when non_query_domain_res is not NULL
non_query_set_only	If TRUE interacting partners of a seed are taken only from non_query_domain_res, if FALSE - both from non_query_domain_res and domain_res. Used only when non_query_domain_res is not NULL
query_domains_only	If TRUE interacting partners of a seed that are taken from non_query_domain_res must be predicted to interact with a seed using domains predicted for query. Used only when non_query_domain_res is not NULL
remove	logical, remove and return InteractionSubsetFASTA_list or just show which sequence and interaction sets have a protein in the set2 associated with domain in the protein in the name of InteractionSubsetFASTA_list entry.

Value

object of class InteractionSubsetFASTA_list filtered for matching protein and 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

listInteractionSubsetFASTA, permutationPval

Examples

forSLIMFinder_Ready = domainProteinPairMatch(forSLIMFinder_Ready, domain_res, remove = T)

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