build_TCGA_Eset: Create an Expression Set from TCGA Data, downloaded from...

In w2felix/TCGADataFelix: Analyzing the TCGA Data according to gene expression and survival

Description

Create an Expression Set from TCGA Data, downloaded from https://gdac.broadinstitute.org/

Usage

build_TCGA_Eset(clinical_file, expression_file, source, skip = FALSE)

Arguments

clinical_file	PATH of the clinical data from TCGA, e.g.: "../../../Projects/TCGA-Elisa/Clinical/LAML.clin.merged.txt"
expression_file	PATH of the expression data from TCGA, e.g.: "../../../Projects/TCGA-Elisa/RNA/LAML.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt"
source	Define the source of the data. "cBio" and "cBio_z_score" for cBioportal Data, "firehose" for Firehose data.
skip	Please Check in the clinical file in which row the header column appears. The amount of rows skiped should be entered as e.g. skip = 5.

Value

ExpressionSet

Examples

## Not run: 
build_TCGA_Eset(clinical_file <- "../../../Projects/TCGA-Elisa/tcga_KIRC_cBio/data_bcr_clinical_data_patient.txt",
expression_file <- "../../../Projects/TCGA-Elisa/tcga_KIRC_cBio/Kdata_RNA_Seq_v2_mRNA_median_Zscores.txt",
source = "cBio_z_score",
normalization = FALSE)

## End(Not run)

w2felix/TCGADataFelix documentation built on May 19, 2019, 8:24 a.m.