e50-filterCommonGenes: Intersect input data with 10,412 common genes

In estimate: Estimate of Stromal and Immune Cells in Malignant Tumor Tissues from Expression Data

Description

This function unifies different number of genes per platform against 10,412 common genes.

Usage

filterCommonGenes(input.f, output.f, id=c("GeneSymbol", "EntrezID"))

Arguments

input.f	character string specifying name of input file, or data.frame including gene-level expression data
output.f	character string specifying name of output file
id	character string indicating which gene identifier to use when matching.

Details

The number of genes in expression data is different for each platform and this difference influences the computational results of stromal and immune scores. To compare stromal, immune and ESTIMATE scores across different platforms or calculate ESTIMATE-based tumor purity using Affymetrix expression data, users need to unify the gene identifiers of the input data against the common genes. Afterwards, the results of the intersection are written to disk in GCT format.

Author(s)

Kosuke Yoshihara [e-mail]

See Also

outputGCT

Examples

in.file <- system.file("extdata", "sample_input.txt", package="estimate")
out.file <- tempfile(pattern="estimate", fileext=".gct")
filterCommonGenes(in.file, out.file)

estimate documentation built on May 2, 2019, 4:38 p.m.