convert_geneID_to_geneSymbol: convert_geneID_to_geneSymbol

In humayun2017/SPAGI2: SPAGI2: Identification of active signalling pathways for cross-species by integrating gene expression and human protein interaction network

Description

This function converts either a vector of gene IDs, a matrix of gene or a named cell / tissue expression profile or matrix to ensembl IDs

Usage

convert_geneID_to_geneSymbol(
  user.cell.data,
  species = "hsapiens",
  geneSymbol.toMapping = "external_gene_name",
  geneID.forMapping = "ensembl_gene_id",
  collapse.method = "max"
)

Arguments

user.cell.data	Cell/tissue profile with valid gene IDs
species	The species of the given gene IDs or cell/tissue profile, default is "hsapiens"
geneSymbol.toMapping	The valid gene ID names (that has ensembl id mapping in the biomaRt database) to which the user.cell.data will be converted, default is "external_gene_name". For more details to get the valid gene ids for a species please see the find_valid_geneID() function of the package.
geneID.forMapping	The valid gene ID names (that has ensembl id mapping in the biomaRt database) of the user.cell.data, default is "ensembl_gene_id". For more details to get the valid gene ids for a species please see the find_valid_geneID() function of the package.
collapse.method	Used when one external_gene_name has more then one probes, usually two options are used, maximum probe value (i.e., "max") or average of probe values (i.e., "mean"), default is "max".

Details

This function converts gene IDs of a named cell/tissue expression profile to gene symbols

Value

This function returns cell/tissue profiles with converted gene symbols

Examples

query.data<-matrix(sample(1:10, 100, replace=TRUE),10,10)
rownames(query.data)<-c("ENSG00000160202", "ENSG00000109846", "ENSG00000100053", "ENSG00000007372", "ENSG00000181449", "ENSG00000117707", "ENSG00000138083", "ENSG00000150938", "ENSG00000244752", "ENSG00000101144")
colnames(query.data)<-c("cell1", "cell1", "cell1", "cell2", "cell2", "cell2", "cell3", "cell3", "cell3", "cell3")
convert_geneID_to_geneSymbol(query.data)

humayun2017/SPAGI2 documentation built on Aug. 5, 2020, 12:06 a.m.