Generate and Subset a XenaHub Object from 'XenaData'
XenaGenerate(XenaData = UCSCXenaTools::XenaData, subset = TRUE)
XenaData | a |
---|---|
subset | logical expression indicating elements or rows to keep. |
a XenaHub object.
Shixiang Wang [email protected]
# 1 get all datasets XenaGenerate()#> class: XenaHub #> hosts(): #> https://ucscpublic.xenahubs.net #> https://tcga.xenahubs.net #> https://gdc.xenahubs.net #> https://icgc.xenahubs.net #> https://toil.xenahubs.net #> https://pancanatlas.xenahubs.net #> https://xena.treehouse.gi.ucsc.edu:443 #> https://pcawg.xenahubs.net #> https://atacseq.xenahubs.net #> https://singlecellnew.xenahubs.net #> https://kidsfirst.xenahubs.net #> https://tdi.xenahubs.net #> cohorts() (155 total): #> Breast Cancer Cell Lines (Neve 2006) #> Glioma (Kotliarov 2006) #> Lung Cancer CGH (Weir 2007) #> ... #> Pediatric Brain Tumor Atlas: PNOC #> Pediatric Brain Tumor Atlas: CBTTC #> datasets() (1679 total): #> ucsfNeve_public/ucsfNeveExp_genomicMatrix #> ucsfNeve_public/ucsfNeve_public_clinicalMatrix #> kotliarov2006_public/kotliarov2006_genomicMatrix #> ... #> TDI/mmc1_sampleLevel.txt #> TDI/iSC_cluster.txt# 2 get TCGA BRCA XenaGenerate(subset = XenaCohorts == "TCGA Breast Cancer (BRCA)")#> class: XenaHub #> hosts(): #> https://tcga.xenahubs.net #> cohorts() (1 total): #> TCGA Breast Cancer (BRCA) #> datasets() (24 total): #> RABIT/separate_processed/RABIT_BRCA.HiSeq #> RABIT/separate_processed/RABIT_BRCA.Agilent #> RABIT/separate_processed/RABIT_BRCA.HiSeq.V2 #> ... #> PanCan33_ssGSEA_1387GeneSets_NonZero_sample_level_Z/BRCA_PanCan33_ssGSEA_1387GeneSets_NonZero_sample_level_Z.txt #> survival/BRCA_survival.txt#> class: XenaHub #> hosts(): #> https://tcga.xenahubs.net #> https://gdc.xenahubs.net #> https://atacseq.xenahubs.net #> cohorts() (2 total): #> TCGA Breast Cancer (BRCA) #> GDC TCGA Breast Cancer (BRCA) #> datasets() (44 total): #> RABIT/separate_processed/RABIT_BRCA.HiSeq #> RABIT/separate_processed/RABIT_BRCA.Agilent #> RABIT/separate_processed/RABIT_BRCA.HiSeq.V2 #> ... #> brca/pam50 #> brca/TCGA-BRCA.methylation450.tsv