tcgaTableGenerator: Generate gene/microRNA expression matrix from single...

In YC3/mirNet: microRNA netowrk analyses

Description

tcgaTableGenerator Generates gene/microRNA expression matrix from single sequencing data files downloaded from GDC Data Portal. The MANIFEST.txt file should be in the same directory.

Usage

tcgaTableGenerator(dataDir, dataType)

Arguments

dataDir	The directory of downloaded sequencing data files as well as the MANIFEST.txt file.
dataType	A string, 'microRNA' for microRNA-seq data or 'mRNA' for RNA-seq data.

Value

A gene/microRNA expression data matrix, with rows referring to genes/microRNAs and columns to samples.

Examples

tcgaTableGenerator(dataDir = './TCGA_RNAseq_LUAD', dataType = 'mRNA')
tcgaTableGenerator(dataDir = './TCGA_miRNAseq_LUAD', dataType = 'microRNA')

YC3/mirNet documentation built on Sept. 3, 2020, 3:25 a.m.