geneMatch: geneMatch

In huangwb8/GSClassifier: Gene Signature Classifier

geneMatch

Description

Match the incoming data to what was used in training

Usage

geneMatch(
  X,
  geneAnnotation = NULL,
  geneid = "ensembl",
  matchmode = c("fix", "free")[1]
)

Arguments

X	gene expression matrix, genes in rows, samples in columns
geneAnnotation	A data frame with ENSEMBL, SYMBOL and ENTREZID of the genes in geneSet
geneid	type of gene id in X. One of 'symbol', 'entrez' and 'ensembl'.
matchmode	If your genes belong to ENSEMBL, SYMBOL or ENTREZ, you should set matchmode = 'fix', in which all genes would be aligned to ENSEMBL. 'matchmode = free' is a legacy feature, which means that you have to convert your genes into the same annotation type of the pre-trained GSClassifier model.

Value

Matched index of genes to the expression matrix.

huangwb8/GSClassifier documentation built on July 12, 2024, 5:10 p.m.