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Fix: UpdateSymbolList incorrectly renames genes #8179

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Fix: UpdateSymbolList incorrectly renames genes #8179

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2909b1c
add check
samuel-marsh Dec 12, 2023
722086f
update module score usage
samuel-marsh Dec 12, 2023
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7 changes: 6 additions & 1 deletion R/utilities.R
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Original file line number Diff line number Diff line change
Expand Up @@ -221,7 +221,7 @@ AddModuleScore <- function(
if (search) {
tryCatch(
expr = {
updated.features <- UpdateSymbolList(symbols = missing.features, ...)
updated.features <- UpdateSymbolList(object = object, symbols = missing.features, ...)
names(x = updated.features) <- missing.features
for (miss in names(x = updated.features)) {
index <- which(x == miss)
Expand Down Expand Up @@ -1726,6 +1726,7 @@ SetQuantile <- function(cutoff, data) {
#' }
#'
UpdateSymbolList <- function(
object,
symbols,
timeout = 10,
several.ok = FALSE,
Expand All @@ -1740,6 +1741,10 @@ UpdateSymbolList <- function(
verbose = verbose,
...
))

# avoid incorrect renaming
new.symbols <- new.symbols[!new.symbols %in% Features(object)]

if (length(x = new.symbols) < 1) {
warning("No updated symbols found", call. = FALSE, immediate. = TRUE)
} else {
Expand Down