labelKeep: Label rows to keep based on minimal count

In fishpond: Fishpond: differential transcript and gene expression with inferential replicates

Description

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.

Usage

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)

fishpond documentation built on Nov. 8, 2020, 7:54 p.m.