README.md

In aaronwolen/tcgatools: TCGA tools

tcgatools

A collection of small tools for working with data from The Cancer Genome Atlas.

Installation

install.packages("devtools")
devtools::install_github("aaronwolen/tcgatools")

Features

Currently, the only useful functionality provided is the ability to parse and annotate TCGA barcodes.

barcodes <- c("TCGA-G9-6361-01A-21R-1965-07",
              "TCGA-HC-7740-11A-01R-2118-07")

Parse:

parse_barcodes(barcodes)

##   project tss participant sample vial portion analyte plate center
## 1    TCGA  G9        6361     01    A      21       R  1965     07
## 2    TCGA  HC        7740     11    A      01       R  2118     07

Annotate:

parse_barcodes(barcodes, annotations = "long")

|project |tss |disease |bcr |participant |sample |vial |portion |analyte |plate |center |center.type | |:-------|:---------------------------------|:-----------------------|:---|:-----------|:-------------------|:----|:-------|:-------|:-----|:----------------------------|:--------------------------------------| |TCGA |Roswell Park |Prostate adenocarcinoma |IGC |6361 |Primary solid Tumor |A |21 |RNA |1965 |University of North Carolina |Cancer Genomic Characterization Center | |TCGA |International Genomics Consortium |Prostate adenocarcinoma |IGC |7740 |Solid Tissue Normal |A |01 |RNA |2118 |University of North Carolina |Cancer Genomic Characterization Center |

aaronwolen/tcgatools documentation built on May 10, 2019, 4:05 a.m.