assignSubtypes,SurvivalExperiment,data.frame-method {PDATK} | R Documentation |
Assign Subtype Annotations to a SurvivalExperiment Object
## S4 method for signature 'SurvivalExperiment,data.frame' assignSubtypes( object, subtypes, ..., sampleCol = "sample_name", subtypeCol = "subtype" )
object |
A |
subtypes |
A |
... |
Force subsequent arguments to be named. Not used. |
sampleCol |
A |
subtypeCol |
A |
The SurvivalExperiment
with the subtypes in the subtypes
column
of the colData slot and a metadata item, hasSubtypes
, set to TRUE.
data(sampleICGCmicro) data(cohortSubtypeDFs) cohortList <- assignSubtypes(sampleICGCmicro, subtypes=cohortSubtypeDFs$ICGCMICRO, sampleCol='sample_name', subtypeCol='subtype')