getTCGAdata | R Documentation |
This is the most useful function for user to download common
TCGA datasets, it is similar to getFirehoseData
function in RTCGAToolbox
package.
getTCGAdata( project = NULL, clinical = TRUE, download = FALSE, forceDownload = FALSE, destdir = tempdir(), mRNASeq = FALSE, mRNAArray = FALSE, mRNASeqType = "normalized", miRNASeq = FALSE, exonRNASeq = FALSE, RPPAArray = FALSE, ReplicateBaseNormalization = FALSE, Methylation = FALSE, MethylationType = c("27K", "450K"), GeneMutation = FALSE, SomaticMutation = FALSE, GisticCopyNumber = FALSE, Gistic2Threshold = TRUE, CopyNumberSegment = FALSE, RemoveGermlineCNV = TRUE, ... )
project |
default is |
clinical |
logical. if |
download |
logical. if |
forceDownload |
logical. if |
destdir |
specify a location to store download data. Default is system temp directory. |
mRNASeq |
logical. if |
mRNAArray |
logical. if |
mRNASeqType |
character vector. Can be one, two or three
in |
miRNASeq |
logical. if |
exonRNASeq |
logical. if |
RPPAArray |
logical. if |
ReplicateBaseNormalization |
logical. if |
Methylation |
logical. if |
MethylationType |
character vector. Can be one or two in |
GeneMutation |
logical. if |
SomaticMutation |
logical. if |
GisticCopyNumber |
logical. if |
Gistic2Threshold |
logical. if |
CopyNumberSegment |
logical. if |
RemoveGermlineCNV |
logical. if |
... |
other argument to |
TCGA Common Data Sets are frequently used for biological analysis.
To make easier to achieve these data, this function provide really easy
options to choose datasets and behavior. All availble information about
datasets of TCGA can access vis availTCGA()
and check with showTCGA()
.
if download=TRUE
, return data.frame
from XenaDownload
,
otherwise return a list including XenaHub
object and datasets information
Shixiang Wang w_shixiang@163.com
###### get data, but not download # 1 choose project and data types you wanna download getTCGAdata(project = "LUAD", mRNASeq = TRUE, mRNAArray = TRUE, mRNASeqType = "normalized", miRNASeq = TRUE, exonRNASeq = TRUE, RPPAArray = TRUE, Methylation = TRUE, MethylationType = "450K", GeneMutation = TRUE, SomaticMutation = TRUE) # 2 only choose 'LUAD' and its clinical data getTCGAdata(project = "LUAD") ## Not run: ###### download datasets # 3 download clinical datasets of LUAD and LUSC getTCGAdata(project = c("LUAD", "LUSC"), clinical = TRUE, download = TRUE) # 4 download clinical, RPPA and gene mutation datasets of LUAD and LUSC # getTCGAdata(project = c("LUAD", "LUSC"), clinical = TRUE, RPPAArray = TRUE, GeneMutation = TRUE) ## End(Not run)
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