sampleList: Generate List of Treatment vs. Control Samples

In yduan004/signatureSearchData: Datasets for signatureSearch package

Generate List of Treatment vs. Control Samples

Description

This function generates a list of treatment samples and control samples CEL ids for each compound treatment from the experiment annotation of CMAP02 instances. For more context of the CMAP02 database, please consult the vignette of this package.

Usage

sampleList(cmap, myby)

Arguments

cmap	data.frame containing experiment information of CMAP02 instances
myby	"CMP" or "CMP_CELL", "CMP": by compound treatments in all cells; "CMP_CELL": by compound treatments in individual cell

Value

a list object containing treatment samples and control samples ids for each compound treament.

Examples

path <- system.file("extdata", "cmap_instances_02.txt", package="signatureSearchData")
cmap_inst <- read.delim(path, check.names=FALSE) 
comp_list <- sampleList(cmap_inst, myby="CMP_CELL")

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