Generate and Subset a XenaHub Object from 'XenaData'

XenaGenerate(XenaData = UCSCXenaTools::XenaData, subset = TRUE)

Arguments

XenaData

a data.frame. Default is data(XenaData). The input of this option can only be data(XenaData) or its subset.

subset

logical expression indicating elements or rows to keep.

Value

a XenaHub object.

Author

Shixiang Wang [email protected]

Examples

# 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 #> cohorts() (157 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() (1675 total): #> ucsfNeve_public/ucsfNeveExp_genomicMatrix #> ucsfNeve_public/ucsfNeve_public_clinicalMatrix #> kotliarov2006_public/kotliarov2006_genomicMatrix #> ... #> CBTTC/Participants.txt #> CBTTC/survival.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
# 3 get all datasets containing BRCA XenaGenerate(subset = grepl("BRCA", XenaCohorts))
#> 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