compare_to_training_labels: Compare the subtypeCMS.RF assigned nearest subtypes to the RF...

In aeolianine/CRCsubtyping: Subtyping Colorectal Expression Data

Compare the subtypeCMS.RF assigned nearest subtypes to the RF model (gold reference) training labels. This is only possible for datasets that are used within the reference set. Note: Currently only TCGA is implemented.

Description

Compare the subtypeCMS.RF assigned nearest subtypes to the RF model (gold reference) training labels. This is only possible for datasets that are used within the reference set. Note: Currently only TCGA is implemented.

Usage

compare_to_training_labels(resRF, whichDataset = NULL)

Arguments

resRF	- output of subtypeCMS.RF
whichDataset	- currently only "TCGA" is a valid input

Value

table (data.frame) of subtypes, training labels and posterior probabilities for samples that do not have matching labels; also a message with the percentage of matching sample labels

Examples

mat = get_TCGA_synapse()
resRF = subtypeCMS.RF(mat)
compare_to_training_labels(resRF, whichDataset = 'TCGA')

aeolianine/CRCsubtyping documentation built on Jan. 13, 2023, 12:16 p.m.