bindMSI: bind MSI data to a SummarizedExperiment

In vjcitn/BiocOncoTK: Bioconductor components for general cancer genomics

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

vjcitn/BiocOncoTK documentation built on Feb. 14, 2023, 11:56 p.m.