meanExpr: Calculate Mean Value for Replicated Samples

View source: R/meanExpr.R

meanExprR Documentation

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