Generate and Subset a XenaHub Object from 'XenaData'

Source: R/XenaGenerate.R

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
#>   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
# 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