subSetNA: sets NTP results to NA based on p-value cutoff

In peterawe/CMScaller: CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

Description

sets ntp predictions to NA based on p-value or FDR thresholds

Usage

subSetNA(res, pValue = 1, FDR = 1, verbose = TRUE)

Arguments

res	a data frame, result from ntp function.
pValue	a numeric, predictions with higher p-values are set to NA.
FDR	a numeric, predictions with higher FDR are set to NA.
verbose	logical, whether console messages are to be displayed.

Details

Replaces low-confidence predictions with NA.

Value

A data.frame where res$prediction's are set to NA based on p-value or FDR threshold.

Examples

emat <- ematAdjust(crcTCGAsubset, normMethod = "quantile")
res <- ntp(emat, templates.CMS, doPlot=TRUE, nPerm=100)
res <- subSetNA(res, pValue=.1)
res <- subSetNA(res, FDR=.1)
table(res$prediction, useNA="always")

peterawe/CMScaller documentation built on June 13, 2020, 4:49 a.m.