bindMSI: bind MSI data to a SummarizedExperiment
In BiocOncoTK: Bioconductor components for general cancer genomics

Description Usage Arguments Value Note Examples

bind MSI data to a SummarizedExperiment

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

`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

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.

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.