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Updated NEWS again.
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LTLA committed Sep 6, 2024
1 parent 0cb7796 commit edf6951
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2 changes: 1 addition & 1 deletion R/SingleR.R
Original file line number Diff line number Diff line change
Expand Up @@ -114,7 +114,7 @@ SingleR <- function(
for (rr in tmp.ref) {
keep <- rownames(test) %in% rownames(rr)
if (!all(keep)) {
test <- DelayedArray(test)[keep,,drop=FALSE]
test <- DelayedArray(test)[keep,,drop=FALSE] # only keeping the intersection, for safety's sake - see ?combineRecomputedResults.
}
}
if (nrow(test) == 0) {
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4 changes: 4 additions & 0 deletions inst/NEWS.Rd
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Expand Up @@ -8,6 +8,10 @@ This is also checked against \code{rownames(test)} in \code{classifySingleR()} t
\item Restored the \code{BNPARAM=} argument in \code{trainSingleR()}, to enable more fine-grained specification of neighbor search algorithms.
The \code{approximate=} argument is deprecated.
\item Soft-deprecated \code{check.missing=} in \code{classifySingleR()} and \code{combineRecomputedResults()}.
This is because any filtering will cause a mismatch between the row names of \code{tests} and the \code{test.genes} in \code{trained}.
Rather, filtering should be done prior to \code{trainSingleR()}, as is done in the main \code{SingleR()} function.
}}
\section{Version 2.0.0}{\itemize{
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