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addresses issue 168 by parameterizing checkAnnots rnktype #432

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addresses issue 168 by parameterizing checkAnnots rnktype #432

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: SCENIC
Type: Package
Title: SCENIC (Single Cell rEgulatory Network Inference and Clustering)
Version: 1.3.1
Version: 1.3.1.9001
Date: 2022-05-02
Author: Sara Aibar, Carmen Bravo, Stein Aerts.
Laboratory of Computational Biology, KU Leuven Center for Human Genetics.
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6 changes: 3 additions & 3 deletions R/class_ScenicOptions.R
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Expand Up @@ -452,7 +452,7 @@ initializeScenic <- function(org=NULL, dbDir="databases", dbs=NULL, datasetTitle

## Check if motif annotation and rankings potentially match
motifAnnot <- getDbAnnotations(object)
featuresWithAnnot <- checkAnnots(object, motifAnnot)
featuresWithAnnot <- checkAnnots(object, motifAnnot, col = dbIndexCol)
if(any(featuresWithAnnot == 0)) message("Missing annotations for: \n", paste("\t", names(which(featuresWithAnnot==0))))

## Return
Expand Down Expand Up @@ -494,12 +494,12 @@ dbLoadingAttempt <- function(dbFilePath, indexCol='features'){

#' @rdname ScenicOptions-class
#' @export
checkAnnots <- function(object, motifAnnot)
checkAnnots <- function(object, motifAnnot, col)
{
allFeaturesInAnnot <- unlist(motifAnnot[,1]) # motif or track
featuresWithAnnot <- lapply(getDatabases(object), function(dbFile)
{
rnktype = "features" #TODO: add as option for custom dbs
rnktype = col #TODO: add as option for custom dbs
nRnks <- getRanking(RcisTarget::importRankings(dbFile, columns = rnktype))
nRnks <- dplyr::pull(nRnks, rnktype)

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2 changes: 1 addition & 1 deletion R/runSCENIC_2_createRegulons.R
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Expand Up @@ -79,7 +79,7 @@ runSCENIC_2_createRegulons <- function(scenicOptions,
})))

## Check if annotation and rankings (potentially) match:
featuresWithAnnot <- checkAnnots(scenicOptions, motifAnnot)
featuresWithAnnot <- checkAnnots(scenicOptions, motifAnnot, col = dbIndexCol)
if(any(featuresWithAnnot == 0)) warning("Missing annotations\n", names(which(rankingsInDb==0)))

### Filter & format co-expression modules
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