plotL1000comparison {cTRAP} | R Documentation |
Plot L1000 data comparison
plotL1000comparison(object, perturbationID, topGenes = TRUE)
object |
|
perturbationID |
Character: perturbation identifier |
topGenes |
Boolean: plot top ( |
Plot illustrating the comparison with L1000 data
data("l1000perturbationsKnockdown") cellLine <- "HepG2" compareKnockdown <- list() # Compare against L1000 using Spearman correlation compareKnockdown$spearman <- compareAgainstL1000( diffExprStat, l1000perturbationsKnockdown, cellLine, method="spearman") # Compare against L1000 using Pearson correlation compareKnockdown$pearson <- compareAgainstL1000( diffExprStat, l1000perturbationsKnockdown, cellLine, method="pearson") # Compare against L1000 using gene set enrichment analysis (GSEA) with the top # and bottom 150 genes compareKnockdown$gsea <- compareAgainstL1000( diffExprStat, l1000perturbationsKnockdown, cellLine, method="gsea", geneSize=150) EIF4G1knockdown <- grep("EIF4G1", compareKnockdown$gsea$genes, value=TRUE) plotL1000comparison(compareKnockdown$spearman, EIF4G1knockdown) plotL1000comparison(compareKnockdown$pearson, EIF4G1knockdown) plotL1000comparison(compareKnockdown$gsea, EIF4G1knockdown)