bindMSI {BiocOncoTK} | R Documentation

## bind MSI data to a SummarizedExperiment

### Description

bind MSI data to a SummarizedExperiment

### Usage

    bindMSI(se, useDing = TRUE, onlyHL = TRUE)

### Arguments

`se` | SummarizedExperiment instance
`useDing` | logical(1) if TRUE, use MSIsensor outputs from Ding et al. Cell 2018, otherwise use firehose labelings msi-h,msi-l
`onlyHL` | logical(1) if TRUE, retain only msi-h, msi-l records; ignored if useDing is TRUE

### Value

SummarizedExperiment instance with expanded colData, samples limited to those with microsatellite instability values. The additional variable is called 'msiTest' and is numerical if useDing is TRUE and is character (msi-h,l,s) otherwise.

### Note

This function adds the column `msiTest` to `colData(se)`. The contents of the column are given by `fireMSI`. Samples in `se` that do not correspond to a row of `fireMSI` are dropped. If there is already a column named `msiTest` in `colData(se)`, it is replaced and samples are filtered as described, and a message is given. If none of the samples in `se` have rows in `fireMSI`, an error is thrown.

### Examples

    bindMSI

[Package BiocOncoTK version 1.2.1 Index]