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. *OF NOTE:* The MSIsensor data from Ding's cell paper (see help(dingMSI) for URL) provides the participant barcode. The participant barcode is a substring of the sample barcode. Be sure to filter the input SummarizedExperiment to include only tumor samples, using the substr(colnames(se),14,15) (values "10"..."14" correspond to normal, non-tumor samples.) Additionally, bindMSI will only work if the colnames of the (filtered) SummarizedExperiment have been truncated to the participant barcode, that is, the first 12 characters of the sample barcode.

### Examples

    bindMSI

[Package BiocOncoTK version 1.12.1 Index]