doc/TCGA.R

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----eval=FALSE---------------------------------------------------------------
#  setwd("yourworkdir")
#  currentwd=getwd()
#  #gdc-client.exe,gdc_manifest.txt in yourworkdir
#  getdata("gdc-client.exe","gdc_manifest.txt")

## ----eval=FALSE---------------------------------------------------------------
#  unzipData(currentwd)

## ----eval=FALSE---------------------------------------------------------------
#  generateMatrix(currentwd)

## ----eval=FALSE---------------------------------------------------------------
#  metaAnnotation(currentwd,"metadata.cart.xxxx.json")

## ----eval=FALSE---------------------------------------------------------------
#  corSamples(currentwd)

## ----eval=FALSE---------------------------------------------------------------
#  DEGsTCGA(currentwd)

## ----eval=FALSE---------------------------------------------------------------
#  DEGsVisualization(currentwd, log2FC=2, pvalue=0.05)

## ----eval=FALSE---------------------------------------------------------------
#  DEGsGeneSymbol(currentwd)

## ----eval=FALSE---------------------------------------------------------------
#  tcgaEnrichment(currentwd, pvalue=0.05)

## ----eval=FALSE---------------------------------------------------------------
#  tcgaClinic(currentwd, "clinic.tsv", transfromed = T, groupby = 0.5)
#  
dming1024/TCGApackages0226 documentation built on April 9, 2021, 7:48 a.m.