assignSubtypes-CohortList-list-method: Assign Subtype Annotations to a SurvivalExperiment Object
In bhklab/PDATK: Pancreatic Ductal Adenocarcinoma Tool-Kit

Description Usage Arguments Value Examples

Assign Subtype Annotations to a SurvivalExperiment Object

## S4 method for signature 'CohortList,list'
assignSubtypes(
  object,
  subtypes,
  ...,
  sampleCol = "sample_name",
  subtypeCol = "subtype"
)

`object`	A `CohortList`.
`subtypes`	A `list` of `data.frame` objects, one per cohort, with to subtypes to assign to the colData slot of cohorts with a matching name.
`...`	Catch unnamed parameters. Not used.
`sampleCol`	A `character` vector indicating the name of the colum with sample identifiers in the subtype column. Must match the name of the sample identifier in colData.
`subtypeCol`	A `character` vectoring indicating the name of the column with the subtype labels in the `subtypes` `data.frame`.

The CohortList with the subtypes in the subtypes column of the colData slot and a metadata item, hasSubtypes, set to TRUE for each SurvivalExperiment.

data(sampleCohortList)
data(cohortSubtypeDFs)

cohortList <- assignSubtypes(sampleCohortList,
  subtypes=cohortSubtypeDFs[names(sampleCohortList)],
  sampleCol='sample_name',
  subtypeCol='subtype')