Signature_Match: Find signature genes' positions in gene expression data

In tdw1221/NITUMID: Non-negative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution

Description

'Signature_Match' takes the input gene expression data and a vector of signature gene symbols, return signature genes' positions in data matrix, as well as those not-matched signature genes.

Usage

Signature_Match(gene_expression, signature_genes,
  signature_genes_alias = NULL)

Arguments

gene_expression	this should be a numeric matrix whose columns are samples and rows are genes, its row names should be genes symbol
signature_genes	this should be a vector of string/character speciying signature gene symbols default value is our generic signature genes list
signature_genes_alias	this optional argument allows you to give signature genes' alias, default is NULL. this also should be a vector of string/character, same length as signature_genes, those who don't have an alias should be set as NA.

Value

'Signature_Match' returns a list consists of two elements: 'matched_index' is a vector same length as signature genes its each entry specifying the corresponding signature genes' positions in 'gene_expression', for those genes don't present in data matrix, its corresponding entries are left with 1221; 'missing_row_index' is a vector indicating which genes are not found in 'gene_expression'

Examples

data is needed otherwise it won't run, the second example won't work because the alias vector has one non-character entry
(having NAs in signature_genes_alias is fine)
 Signature_Match(gene_expression_matrix,signature_genes=c("MIA","EGFR") )
 ## Not run: 
 Signature_Match(gene_expression_matrix,signature_genes=c("MIA","EGFR"),signature_genes_alias=c(NA,2) )
 
## End(Not run)
 @export

tdw1221/NITUMID documentation built on May 31, 2019, 1:54 a.m.