load_cohort: Load dataframe clinical info and optional RNASeq and CNV data

In tjbencomo/TBmisc: Miscellaneous functions for working with biomedical data

Description

Load dataframe clinical info and optional RNASeq and CNV data

Usage

load_cohort(cancer, data.dir, genes = NULL, include.cnv = TRUE,
  include.rna = TRUE, file = NULL)

Arguments

cancer	TCGA study (use acronym i.e. SKCM)
data.dir	Directory where the data files are stored
genes	Genes to include in dataframe. NULL loads all genes
include.cnv	Whether to load copy number data
include.rna	Whether to load rnaseq data
file	Filename of the file containing clinical data

Value

Dataframe where each row is a patient sample with columns containing clinical info as well as optional RNASeq/CNV data. All patients have complete Overall Survival data. Solid Tissue Normal samples are not included.

tjbencomo/TBmisc documentation built on May 16, 2019, 4:10 a.m.