ntpMakeTemplates: nearest template prediction templates

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

Description

Reformats list of gene sets or results from subDEG into prediction templates for ntp.

Usage

ntpMakeTemplates(
  geneSets,
  resDEG = TRUE,
  lfc = 1,
  padj = 0.1,
  topN = NULL,
  verbose = getOption("verbose", FALSE)
)

Arguments

geneSets	list of vectors with gene identifiers (coerced to character).
resDEG	logical, if geneSets is result from subDEG.
lfc	numeric, log2fold-change threshold (only applicable if resDEG=TRUE).
padj	numeric, p_{adj}-value threshold (only applicable if resDEG=TRUE).
topN	integer, (maximum) number of genes per class.
verbose	logical, whether console messages are to be displayed.

Value

A data.frame formated as templates for ntp.

See Also

ntp, subDEG

Examples

deg <- subDEG(crcTCGAsubset, crcTCGAsubset$CMS, doVoom=TRUE, sortBy="B")
tmp <- ntpMakeTemplates(deg, topN=25)
table(tmp$class)

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