TCGAbiolinks (version 1.2.5)

TCGAprepare_elmer: Prepare the data for ELEMR package

Description

Prepare the data for ELEMR package

Usage

TCGAprepare_elmer(data, platform, met.na.cut = 0.2, save = FALSE)

Arguments

data

A data frame or summarized experiment from TCGAPrepare

platform

platform of the data. Example: "HumanMethylation450", "IlluminaHiSeq_RNASeqV2"

met.na.cut

Define the percentage of NA that the line should have to remove the probes for humanmethylation platforms.

save

Save object? Default: FALSE. Names of the files will be: "Exp_elmer.rda" (object Exp) and "Met_elmer.rda" (object Met)

Value

Matrix prepared for fetch.mee function

Examples

df <- data.frame(runif(200, 1e5, 1e6),runif(200, 1e5, 1e6))
rownames(df) <- sprintf("?|%03d", 1:200)
df <- TCGAprepare_elmer(df,platform="IlluminaHiSeq_RNASeqV2")