check_gset_nms: Checks 'gset_nms'

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Checks gset_nms

Description

It is OK that gset_nms not in "go_sets", "c2_msig", "kegg_sets", "kinsub" as custom gene sets may be applied.

Usage

check_gset_nms(gset_nms)

Arguments

gset_nms

Character string or vector containing the shorthanded name(s), full file path(s), or both, to gene sets for enrichment analysis. For species among "human", "mouse", "rat", the default of c("go_sets", "c2_msig", "kinsub") will utilize terms from gene ontology (GO), molecular signatures (MSig) and kinase-substrate network (PSP Kinase-Substrate). Custom GO, MSig and other data bases at given species are also supported. See also: prepGO for the preparation of custom GO; prepMSig for the preparation of custom MSig. For other custom data bases, follow the same format of list as GO or MSig.

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.