labelKeep {fishpond} | R Documentation

## Label rows to keep based on minimal count

### 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)

[Package fishpond version 1.8.0 Index]