MarrFilterData {marr} | R Documentation

## Filter by Maximum Rank Reproducibility

### Description

Filters `Marr` object according to the Maximum Rank Reproducibility of the features, samples pairs, or both. Features are removed if their reproducibility per sample pair is less than `pFeatures`. Samples are removed if their sample pair reproducibility per feature is less than `pSamplepairs` for all pairings of that sample and the other samples in the set.

### Usage

    MarrFilterData(object, by = c("both", "features", "samplePairs"))

### Arguments

`object` | a Marr object from `Marr`
`by` | String specifying which reproducibility values to filter by. Options include "features" to filter features according to their reproducibility, "samplePairs" to filter samples according to the reproducibility of sample pairs, or "both" to filter both features and sample pairs according to their respective reproducibility. Default is "both".

### Value

A list of `data.frame`'s or a `SummarizedExperiment`. If a `data.frame` was originally input into the `Marr` function, a list with three elements, `filteredData`, `removedSamples`, and `removedFeatures`, will be returned. If a `SummarizedExperiment` was originally input, output will be a `SummarizedExperiment` with the assay filtered and with two metadata objects, `removedSamples` and `removedFeatures` added.

### Examples

    data <- matrix(rnorm(2400), nrow=200, ncol=12)
    data_Marr <- Marr(object = data, pSamplepairs=0.75,
                      pFeatures=0.75, alpha=0.05)
    MarrFilterData(data_Marr, by = "both")

[Package marr version 1.4.0 Index]