TCGAquery_recount2: Query gene counts of TCGA and GTEx data from the Recount2...

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Query gene counts of TCGA and GTEx data from the Recount2 project

Description

TCGArecount2_query queries and downloads data produced by the Recount2 project. User can specify which project and which tissue to query

Usage

TCGAquery_recount2(project, tissue = c())

Arguments

project

is a string denoting which project the user wants. Options are "tcga" and "gtex"

tissue

a vector of tissue(s) to download. Options are "adipose tissue", "adrenal gland", "bladder","blood", "blood vessel", "bone marrow", "brain", "breast","cervix uteri", "colon", "esophagus", "fallopian tube","heart", "kidney", "liver", "lung", "muscle", "nerve", "ovary","pancreas", "pituitary", "prostate", "salivary gland", "skin", "small intestine", "spleen", "stomach", "testis", "thyroid", "uterus", "vagina"

Value

List with $subtypes attribute as a dataframe with barcodes, samples, subtypes, and colors. The $filtered attribute is returned as filtered samples with no subtype info

Examples

## Not run: 
 brain.rec<-TCGAquery_recount2(project = "gtex", tissue = "brain")

## End(Not run)

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.