prepareSignature: Prepare an L1000 Signature froma given differential gene...

In CogDisResLab/drugfindR: Investigate iLINCS for candidate repurposable drugs

Prepare an L1000 Signature froma given differential gene expression output

Description

This function takes a differential gene expression output from any pipeline like edgeR or DeSeq2 or any that give you the gene symbol, log_2 fold-change and p-value and transforms that into an L1000 signature for later processing.

Usage

prepareSignature(
  dge,
  geneColumn = "Symbol",
  logfcColumn = "logFC",
  pvalColumn = "PValue"
)

Arguments

dge	A dataframe-like object that has the differential gene expression information
geneColumn	The name of the column that has gene symbols
logfcColumn	The name of the column that has log_2 fold-change values
pvalColumn	The name of the column that has p-values

Value

A tibble with the L1000 signature.

Examples

# Prepare an L1000 signature from a differential gene expression output

inputSignature <- read.table(system.file("extdata",
    "dCovid_diffexp.tsv",
    package = "drugfindR"
), header = TRUE)

signature <- prepareSignature(inputSignature,
    geneColumn = "hgnc_symbol",
    logfcColumn = "logFC", pvalColumn = "PValue"
)

head(signature)

CogDisResLab/drugfindR documentation built on Nov. 19, 2024, 4:17 p.m.