compareAgainstL1000 {cTRAP}R Documentation

Compare against L1000 datasets

Description

Compare against L1000 datasets

Usage

compareAgainstL1000(diffExprGenes, perturbations, cellLine,
  method = c("spearman", "pearson", "gsea"), geneSize = 150,
  pAdjustMethod = "BH")

Arguments

diffExprGenes

Numeric: named vector of differentially expressed genes where the name of the vector are gene names and the values are a statistic that represents significance and magnitude of differentially expressed genes (e.g. t-statistics)

perturbations

l1000perturbations object: file with L1000 loaded perturbations (check loadL1000perturbations)

cellLine

Character: cell line(s)

method

Character: comparison method (spearman, pearson or gsea)

geneSize

Number: top and bottom differentially expressed genes to use for gene set enrichment (GSE) (only used if method is gsea)

pAdjustMethod

Character: method for p-value adjustment (for more details, see p.adjust.methods; only used if method is spearman or pearson)

Value

Data table with correlation or GSEA results comparing differential gene expression values with those associated with L1000 perturbations

Examples

cellLine <- "HepG2"
data("l1000perturbationsSmallMolecules")
perturbations <- l1000perturbationsSmallMolecules
data("diffExprStat")

# Compare against L1000 using Spearman correlation
compareAgainstL1000(diffExprStat, perturbations, cellLine,
                    method="spearman")

# Compare against L1000 using Pearson correlation
compareAgainstL1000(diffExprStat, perturbations, cellLine,
                    method="pearson")

# Compare against L1000 using gene set enrichment analysis (GSEA)
compareAgainstL1000(diffExprStat, perturbations, cellLine, method="gsea")

[Package cTRAP version 1.2.0 Index]