loadCTRPgeneExpression: Load CTRP data

In cTRAP: Identification of candidate causal perturbations from differential gene expression data

Description

If given paths direct to non-existing files, those files will be downloaded

Usage

loadCTRPgeneExpression(
  geneExpressionFile = "CTRP 2.1/geneExpr.txt",
  geneInfoFile = "CTRP 2.1/geneInfo.txt",
  cellLineInfoFile = "CTRP 2.1/cellLineInfo.txt"
)

loadCTRPdrugSensitivity(
  drugSensitivityFile = "CTRP 2.1/drugSensitivity.txt",
  experimentFile = "CTRP 2.1/experimentInfo.txt",
  compoundFile = "CTRP 2.1/compoundInfo.txt"
)

loadCTRPcompoundInfo(compoundFile = "CTRP 2.1/compoundInfo.txt")

loadNCI60geneExpression(
  file = "NCI60/geneExpr.xls",
  cellLineInfoFile = "cellLineInfo.xls"
)

loadGDSC7file(file, filename, type, ...)

loadGDSC7cellLineInfo(file = "GDSC_7/cellLineInfo.xlsx")

loadGDSC7compoundInfo(file = "GDSC_7/compoundInfo.xlsx")

loadGDSC7geneExpression(file = "GDSC_7/geneExpr.txt")

loadGDSC7drugSensitivity(file = "GDSC_7/drugs.xlsx")

Arguments

geneExpressionFile	Character: path to file with gene expression
geneInfoFile	Character: path to file with gene information
cellLineInfoFile	Character: path to file with cell line information
drugSensitivityFile	Character: path to file with drug sensitivity
experimentFile	Character: path to file with experiment information
compoundFile	Character: path to file with compound information
file	Character: file path

Value

Data frame

cTRAP documentation built on Nov. 8, 2020, 10:58 p.m.