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ropensci / UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
https://docs.ropensci.org/UCSCXenaTools
GNU General Public License v3.0
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RemoveGermlineCNV 没有移除种系CNV? #4

Closed ShixiangWang closed 5 years ago

ShixiangWang commented 5 years ago

尊敬的作者，您好，我最近在使用咱们的工具下载拷贝数变异数据，但有个问题想咨询您，我利用

AA=getTCGAdata(project = 'OV',GisticCopyNumber = TRUE, Gistic2Threshold = FALSE,
               download = TRUE, RemoveGermlineCNV = FALSE)

AA=getTCGAdata(project = 'OV',GisticCopyNumber = TRUE, Gistic2Threshold = FALSE,
               download = TRUE, RemoveGermlineCNV = TRUE)

下载的是一样的，其中移除生殖细胞这块一个是FALSE一个是TRUE，是其本身就一样还是怎么样啊？还请给予回答，这个问题对我来说很重要，多谢您啦；

ShixiangWang commented 5 years ago

Gistic 数据并没有移除Germline和没移除的区分，这个可以查看官方页面。

RemoveGermlineCNV 改变的是 CopyNumberSegment 的结果。

> getTCGAdata(project = 'OV', CopyNumberSegment = TRUE, Gistic2Threshold = FALSE,
+                download = FALSE, RemoveGermlineCNV = TRUE)
$Xena
class: XenaHub 
hosts():
  https://tcga.xenahubs.net
cohorts() (1 total):
  TCGA Ovarian Cancer (OV)
datasets() (2 total):
  TCGA.OV.sampleMap/OV_clinicalMatrix
  TCGA.OV.sampleMap/SNP6_nocnv_genomicSegment

$DataInfo
# A tibble: 2 x 20
  XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label Type  AnatomicalOrigin
  <chr>     <chr>         <chr>       <chr>        <chr>       <chr>       <chr> <chr> <chr>           
1 https://… tcgaHub       TCGA Ovari… TCGA.OV.sam… 630         phenotype   Phen… clin… ""              
2 https://… tcgaHub       TCGA Ovari… TCGA.OV.sam… 606         copy numbe… Afte… geno… Ovary           
# … with 11 more variables: SampleType <chr>, Tags <chr>, ProbeMap <chr>, LongTitle <chr>,
#   Citation <chr>, Version <chr>, Unit <chr>, Platform <chr>, ProjectID <chr>, DataType <chr>,
#   FileType <chr>

> getTCGAdata(project = 'OV', CopyNumberSegment = TRUE, Gistic2Threshold = FALSE,
+                download = FALSE, RemoveGermlineCNV = FALSE)
$Xena
class: XenaHub 
hosts():
  https://tcga.xenahubs.net
cohorts() (1 total):
  TCGA Ovarian Cancer (OV)
datasets() (2 total):
  TCGA.OV.sampleMap/OV_clinicalMatrix
  TCGA.OV.sampleMap/SNP6_genomicSegment

$DataInfo
# A tibble: 2 x 20
  XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label Type  AnatomicalOrigin
  <chr>     <chr>         <chr>       <chr>        <chr>       <chr>       <chr> <chr> <chr>           
1 https://… tcgaHub       TCGA Ovari… TCGA.OV.sam… 630         phenotype   Phen… clin… ""              
2 https://… tcgaHub       TCGA Ovari… TCGA.OV.sam… 606         copy numbe… Befo… geno… Ovary           
# … with 11 more variables: SampleType <chr>, Tags <chr>, ProbeMap <chr>, LongTitle <chr>,
#   Citation <chr>, Version <chr>, Unit <chr>, Platform <chr>, ProjectID <chr>, DataType <chr>,
#   FileType <chr>

关于选项的说明，在R里面运行

library(UCSCXenaTools)
?getTCGAdata