buildConsensusGenes: Build Consensus Gene Supersets 'buildConsensusGenes' Combines...

In Famingzhao/ConsensusTME: A Consensus Approach To Tumour Microenvironment Cell Estimation

Description

Build Consensus Gene Supersets buildConsensusGenes Combines pre-processed signatures and filters to create curated gene sets.

Usage

buildConsensusGenes(matchedSigs, consCancerType = cancerAll,
  immuneFilter = NULL, stromalFilter = NULL, immuneScore = TRUE,
  unfilteredGeneSet = NULL)

Arguments

matchedSigs	list of pre-processed signatures with consistant cell type nomenclature
consCancerType	TCGA cancer types to produce gene sets for if no cancer type is specified Default: All TCGA cancer types.
immuneFilter	list of genes to filter immune gene sets by. If NULL - methodSignatures$ImmuneGenes is used (list of immune genes with negative correlation with tumour purity for each tcga cancer type). N.B. Must have two columns: "Gene_Symbol" & "Cancer".
stromalFilter	list of genes to filter stromal gene sets by. If NULL - methodSignatures$ESTIMATE is used (list of ESTIMATE's stromal genes with negative correlation with tumour purity for each tcga cancer type). N.B. Must have two columns: "Gene_Symbol" & "Cancer".
immuneScore	logical, when TRUE (default) an Immune Score is produced representing overall level of immune infiltration for each sample.
unfilteredGeneSet	logical, include geneset without cancer specific filtering. If left empty & more than one cancer type has been specified defaults to TRUE otherwise defaults to FALSE.

Value

returns consensusGeneSets

Famingzhao/ConsensusTME documentation built on Dec. 17, 2021, 8:23 p.m.