l1000perturbationsSmallMolecules {cTRAP} | R Documentation |
L1000 perturbations sample for small molecules obtained by running the following code:
l1000metadataSmallMolecules <- filterL1000metadata( l1000metadata, cellLine="HepG2", timepoint="24 h", dosage="5 \U00B5M", # \U00B5 is the unicode code for the micro symbol perturbationType="Compound") l1000zscores <- downloadL1000data("l1000zscores.gctx", "zscores", l1000metadataSmallMolecules$sig_id) l1000geneInfo <- downloadL1000data("l1000geneInfo.txt") l1000perturbationsSmallMolecules <- loadL1000perturbations( l1000metadataSmallMolecules, l1000zscores, l1000geneInfo, sanitizeCompoundNames=TRUE) # Select only some perturbations (to reduce file size) data("diffExprStat") compareSmallMolecule <- list() compareSmallMolecule$spearman <- compareAgainstL1000( diffExprStat, l1000perturbationsSmallMolecules, cellLine, method="spearman") compareSmallMolecule$pearson <- compareAgainstL1000( diffExprStat, l1000perturbationsSmallMolecules, cellLine, method="pearson") compareSmallMolecule$gsea <- compareAgainstL1000( diffExprStat, l1000perturbationsSmallMolecules, cellLine, method="gsea", geneSize=150) genes <- lapply(compareSmallMolecule, "[[", "genes") filter <- c(unlist(lapply(genes, head)), unlist(lapply(genes, tail))) l1000perturbationsSmallMolecules <- l1000perturbationsSmallMolecules[ , filter]