## ---- 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)
#
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