1. gCrisprTools
  2. Commit 631574660f95ab8e16e2b89a2c3fe006fbe9c104
Browse code

vignette bugfix/improved target detection in PRC/ROC

RussBainer authored on 18/05/2021 22:55:06
Showing 4 changed files
R/GeneratePRC.R
History View file @ 6315746
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@@ -28,14 +28,23 @@ ct.PRC <-
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     direction <- match.arg(direction)
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     stopifnot(is(plot.it, 'logical'))
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-
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-    collapse <- ifelse(sum(target.list %in% summaryDF$geneID) > sum(target.list %in% summaryDF$geneSymbol), 'geneID', 'geneSymbol')
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-    simpleDF <- ct.simpleResult(summaryDF, collapse)
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-
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+
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     if(!is.character(target.list)){
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       warning("Supplied target.list is not a character vector. Coercing.")
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       target.list <- as.character(target.list)
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     }
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+
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+    #Infer whether Gsdb is ID or feature centric
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+    gids <- sum(target.list %in% summaryDF$geneID)
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+    gsids <- sum(target.list %in% summaryDF$geneSymbol)
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+
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+    if(all(c(gsids, gids) == 0)){
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+      stop('None of the features in the GeneSetDb are present in either the geneID or geneSymbol slots of the first provided result.')
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+    }
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+
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+    collapse <- ifelse(gids > gsids, 'geneID', 'geneSymbol')
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+    simpleDF <- ct.simpleResult(summaryDF, collapse)
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+
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     present <- intersect(target.list, row.names(simpleDF))
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     if(length(present) != length(target.list)){
R/GenerateROC.R
History View file @ 6315746
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@@ -34,14 +34,23 @@ ct.ROC <-
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     direction <- match.arg(direction)
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     stopifnot(is(plot.it, 'logical'), is(condense, 'logical'))
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-
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-    collapse <- ifelse(sum(target.list %in% summaryDF$geneID) > sum(target.list %in% summaryDF$geneSymbol), 'geneID', 'geneSymbol')
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-    simpleDF <- ct.simpleResult(summaryDF, collapse)
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-
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+
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     if(!is.character(target.list)){
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       warning("Supplied target.list is not a character vector. Coercing.")
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       target.list <- as.character(target.list)
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     }
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+
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+    #Infer whether Gsdb is ID or feature centric
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+    gids <- sum(target.list %in% summaryDF$geneID)
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+    gsids <- sum(target.list %in% summaryDF$geneSymbol)
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+
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+    if(all(c(gsids, gids) == 0)){
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+      stop('None of the features in the GeneSetDb are present in either the geneID or geneSymbol slots of the first provided result.')
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+    }
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+
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+    collapse <- ifelse(gids > gsids, 'geneID', 'geneSymbol')
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+    simpleDF <- ct.simpleResult(summaryDF, collapse)
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+
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     present <- intersect(target.list, row.names(simpleDF))
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     if(length(present) != length(target.list)){
data/essential.genes.RData
History View file @ 6315746
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Binary files a/data/essential.genes.RData and b/data/essential.genes.RData differ
vignettes/gCrisprTools_Vignette.Rmd
History View file @ 6315746
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@@ -311,18 +311,21 @@ In some cases, it may be useful to ask whether a set of known targets is disprop
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 ```{r, fig.width=6, fig.height = 6, warning=FALSE}
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 data("essential.genes", package = "gCrisprTools")  #Artificial list created for demonstration
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 data("resultsDF", package = "gCrisprTools")
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-ROC <- ct.ROC(resultsDF, essential.genes, stat = "deplete.p")
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+ROC <- ct.ROC(resultsDF, essential.genes, 'enrich')
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 str(ROC)
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 ```
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 ```{r, fig.width=6, fig.height = 6, warning=FALSE}
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-PRC <- ct.PRC(resultsDF, essential.genes, stat = "deplete.p")
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+PRC <- ct.PRC(resultsDF, essential.genes, 'enrich')
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 str(PRC)
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 ```
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 Alternatively, the significance of the enrichment within the target set may be assessed directly with `ct.targetSetEnrichment`.
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 ```{r, fig.width=6, fig.height = 6, warning=FALSE}
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+##' tar <-  sample(unique(resultsDF$geneSymbol), 20)
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+##' res <- ct.targetSetEnrichment(resultsDF, tar)
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+
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 targetsTest <- ct.targetSetEnrichment(resultsDF, essential.genes, enrich = FALSE)
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 str(targetsTest)
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 ```