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Fix issues with addmodulescore and addGeneIntegrationMatrix #2321

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Fix issues with addmodulescore and addGeneIntegrationMatrix #2321

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2a71f22
fix bugs with addmodulescore and addGeneIntegrationMatrix
Liuy12 Mar 6, 2026
fdac3be
change function name back to addModuleScore
Liuy12 Mar 6, 2026
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56 changes: 35 additions & 21 deletions R/ModuleScore.R
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Original file line number Diff line number Diff line change
Expand Up @@ -148,32 +148,46 @@ addModuleScore <- function(
#Figure out the index numbers of the selected features within the given matrix
if(grepl(":",unlist(features)[1])){

sname <- stringr::str_split(unlist(features),pattern=":",simplify=TRUE)[,1]
name <- stringr::str_split(unlist(features),pattern=":",simplify=TRUE)[,2]

idx <- lapply(seq_along(name), function(x){
ix <- intersect(
which(tolower(name[x]) == tolower(featureDF$name)),
BiocGenerics::which(tolower(sname[x]) == tolower(featureDF$seqnames))
)
if(length(ix)==0){
.logStop(sprintf("FeatureName (%s) does not exist! See available features using getFeatures()", name[x]), logFile = logFile)
idx <- lapply(seq_along(features), function(x){
sname <- stringr::str_split(features[[x]], pattern=":", simplify=TRUE)[,1]
fname <- stringr::str_split(features[[x]], pattern=":", simplify=TRUE)[,2]

ix <- vapply(seq_along(fname), function(z){
hit <- intersect(
which(tolower(fname[z]) == tolower(featureDF$name)),
BiocGenerics::which(tolower(sname[z]) == tolower(featureDF$seqnames))
)
if(length(hit) == 0) return(NA_integer_)
hit[1]
}, integer(1))

missing <- features[[x]][is.na(ix)]
if(length(missing) > 0){
if(all(is.na(ix))){
.logStop(sprintf("All features (%s) in feature set %s not found! See available features using getFeatures()", paste(missing, collapse = ", "), x), logFile = logFile)
}
.logMessage(sprintf("Warning: %d of %d features not found and will be omitted: %s", length(missing), length(ix), paste(missing, collapse = ", ")), logFile = logFile)
warning(sprintf("Features not found and will be omitted: %s", paste(missing, collapse = ", ")))
ix <- ix[!is.na(ix)]
}
ix
})

}else{

idx <- lapply(seq_along(unlist(features)), function(x){

ix <- which(tolower(unlist(features)[x]) == tolower(featureDF$name))[1]

if(length(ix) == 0){
.logStop(sprintf("FeatureName (%s) no regions found overlapping! See available features using getFeatures()", unlist(features)[x]), logFile = logFile)
idx <- lapply(seq_along(features), function(x){

ix <- match(tolower(features[[x]]), tolower(featureDF$name))
missing <- features[[x]][is.na(ix)]
if(length(missing) > 0){
if(all(is.na(ix))){
.logStop(sprintf("All features (%s) in feature set %s not found! See available features using getFeatures()", paste(missing, collapse = ", "), x), logFile = logFile)
}
.logMessage(sprintf("Warning: %d of %d features not found and will be omitted: %s", length(missing), length(ix), paste(missing, collapse = ", ")), logFile = logFile)
warning(sprintf("Features not found and will be omitted: %s", paste(missing, collapse = ", ")))
ix <- ix[!is.na(ix)]
}

ix

})

}
Expand All @@ -184,16 +198,16 @@ addModuleScore <- function(
stop("Feature Input is Not A GRanges object!")
}

idx <- lapply(seq_along(unlist(features)), function(x){
idx <- lapply(seq_along(features), function(x){

#Check
o <- tryCatch({GenomeInfoDb::seqlevelsStyle(features[[x]]) <- "UCSC"}, warning = function(w) 0, error = function(e) 0)

#Overlaps
ix <- which(overlapsAny(featureData, features[[x]], ignore.strand=TRUE))

if(length(ix)==0){
.logStop(sprintf("FeatureName (%s) does not exist! See available features using getFeatures()", unlist(features)[x]), logFile = logFile)
if(length(ix) == 0){
.logStop(sprintf("All GRanges features in feature set %s have no overlapping regions! See available features using getFeatures()", x), logFile = logFile)
}

ix
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2 changes: 1 addition & 1 deletion R/RNAIntegration.R
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Original file line number Diff line number Diff line change
Expand Up @@ -531,7 +531,7 @@ addGeneIntegrationMatrix <- function(

if(addToArrow){
.logDiffTime(sprintf("%s Seurat TransferData GeneMatrix", prefix), tstart, verbose = verbose, logFile = logFile)
transferParams$refdata <- GetAssayData(subRNA, assay = "RNA", slot = "data")
transferParams$refdata <- GetAssayData(subRNA, assay = "RNA", layer = "data")
gc()
matchedRNA <- do.call(Seurat::TransferData, transferParams)
matchedRNA <- matchedRNA@data
Expand Down