TCGAquery_recount2 {TCGAbiolinks} | R Documentation

## 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)

[Package TCGAbiolinks version 2.18.0 Index]