Label rows to keep based on minimal count

Adds a column keep to mcols(y) that specifies which rows of the SummarizedExperiment will be included in statistical testing. Rows are not removed, just marked with the logical keep.

labelKeep(y, minCount = 10, minN = 3, x)

Arguments

y

a SummarizedExperiment

minCount

the minimum count

minN

the minimum sample size at minCount

x

the name of the condition variable, will use the smaller of the two groups to set minN. Similar to edgeR's filterByExpr, as the smaller group grows past 10, minN grows only by 0.7 increments of sample size

Value

a SummarizedExperiment with a new column keep

in mcols(y)

Examples

y <- makeSimSwishData()
y <- scaleInfReps(y)
y <- labelKeep(y)