compareAgainstL1000 {cTRAP} | R Documentation |
Compare against L1000 datasets
compareAgainstL1000(diffExprGenes, perturbations, cellLine, method = c("spearman", "pearson", "gsea"), geneSize = 150, pAdjustMethod = "BH")
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 |
|
cellLine |
Character: cell line(s) |
method |
Character: comparison method ( |
geneSize |
Number: top and bottom differentially expressed genes to use
for gene set enrichment (GSE) (only used if |
pAdjustMethod |
Character: method for p-value adjustment (for more
details, see |
Data table with correlation or GSEA results comparing differential gene expression values with those associated with L1000 perturbations
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")