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Fix pseudo count #4111

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merged 2 commits into from
Feb 22, 2021
Merged

Fix pseudo count #4111

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e0084ef
fix pseudocount in FindMarkers.Assay
lldelisle Feb 19, 2021
3863336
fix mean.fxn and fc.name in FindMarkers.DimReduc
lldelisle Feb 19, 2021
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6 changes: 5 additions & 1 deletion R/differential_expression.R
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Original file line number Diff line number Diff line change
Expand Up @@ -627,6 +627,7 @@ FindMarkers.Assay <- function(
cells.1 = cells.1,
cells.2 = cells.2,
features = features,
pseudocount.use = pseudocount.use,
mean.fxn = mean.fxn,
fc.name = fc.name,
base = base
Expand Down Expand Up @@ -680,6 +681,7 @@ FindMarkers.DimReduc <- function(
min.cells.group = 3,
pseudocount.use = 1,
mean.fxn = rowMeans,
fc.name = NULL,
...

) {
Expand All @@ -705,7 +707,9 @@ FindMarkers.DimReduc <- function(
object = object,
cells.1 = cells.1,
cells.2 = cells.2,
features = features
features = features,
mean.fxn = mean.fxn,
fc.name = fc.name
)
# subsample cell groups if they are too large
if (max.cells.per.ident < Inf) {
Expand Down