meanExpr: Calculate Mean Value for Replicated Samples

In yduan004/signatureSearchData: Datasets for signatureSearch package

Calculate Mean Value for Replicated Samples

Description

Function averages the normalized gene expression values for different concentrations, treatment times and replicates of compounds and cell types. For more context on this step, please consult the corresponding section in the vignette of this package.

Usage

meanExpr(expr_df, cmap_inst)

Arguments

expr_df	data.frame containing normalized expression values
cmap_inst	data.frame defining experimental conditions

Value

data.frame with mean expression values of replicates

Examples

path <- system.file("extdata", "cmap_instances_02.txt", package="signatureSearchData")
cmap_inst <- read.delim(path, check.names=FALSE) 
expr_df <- as.data.frame(matrix(runif(30), ncol=5))
colnames(expr_df) <- paste0(cmap_inst$perturbation_scan_id[seq_len(5)],".CEL")
mexpr <- meanExpr(expr_df, cmap_inst[seq_len(5),])

yduan004/signatureSearchData documentation built on April 7, 2023, 4:12 a.m.