bindMSI {BiocOncoTK} | R Documentation |
bind MSI data to a SummarizedExperiment
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.
bindMSI