probe2gene: Transform Probe Set to Gene Level Data

In yduan004/signatureSearch_data: Datasets for signatureSearch package

Transform Probe Set to Gene Level Data

Description

Function to transform expression values from probe set to gene level data. If genes are represented by several probe sets then their mean intensities are used. Probe sets not matching any gene ids are removed.

Usage

probe2gene(expr_df, annot)

Arguments

expr_df	data.frame with probe set level expression data
annot	data.frame containing probe set id (in row name slot) to gene entrez id (in first column) mapping information

Value

data.frame with gene level expression values

Examples

expr_df <- data.frame(t1=runif(3), t2=runif(3), row.names=paste0("p", 1:3))
annot <- data.frame(ENTREZID=c("123","123","124"), 
                    SYMBOL=c("g1","g1","g2"),
                    row.names=paste0("p", 1:3))
gdf <- probe2gene(expr_df, annot)

yduan004/signatureSearch_data documentation built on April 7, 2023, 5:02 a.m.