Filter a XenaHub Object

Source: R/XenaFilter.R

One of main functions in UCSCXenatools. It is used to filter XenaHub object according to cohorts, datasets. All datasets can be found at https://xenabrowser.net/datapages/.

XenaFilter(
  x,
  filterCohorts = NULL,
  filterDatasets = NULL,
  ignore.case = TRUE,
  ...
)

Arguments

x

a XenaHub object
filterCohorts

default is NULL. A character used to filter cohorts, regular expression is supported.
filterDatasets

default is NULL. A character used to filter datasets, regular expression is supported.
ignore.case

if FALSE, the pattern matching is case sensitive and if TRUE, case is ignored during matching.
...

other arguments except value passed to base::grep().

Value

a XenaHub object

Author

Shixiang Wang [email protected]

Examples

# operate TCGA datasets
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
xe

#> class: XenaHub 
#> hosts():
#>   https://tcga.xenahubs.net
#> cohorts() (38 total):
#>   TCGA Ovarian Cancer (OV)
#>   TCGA Kidney Clear Cell Carcinoma (KIRC)
#>   TCGA Lower Grade Glioma (LGG)
#>   ...
#>   TCGA Colon Cancer (COAD)
#>   TCGA Formalin Fixed Paraffin-Embedded Pilot Phase II (FPPP)
#> datasets() (715 total):
#>   TCGA.OV.sampleMap/HumanMethylation27
#>   TCGA.OV.sampleMap/HumanMethylation450
#>   TCGA.OV.sampleMap/Gistic2_CopyNumber_Gistic2_all_data_by_genes
#>   ...
#>   TCGA.FPPP.sampleMap/miRNA_HiSeq_gene
#>   TCGA.FPPP.sampleMap/FPPP_clinicalMatrix
# get all names of clinical data
xe2 = XenaFilter(xe, filterDatasets = "clinical")
datasets(xe2)

#>  [1] "TCGA.OV.sampleMap/OV_clinicalMatrix"            
#>  [2] "TCGA.KIRC.sampleMap/KIRC_clinicalMatrix"        
#>  [3] "TCGA.LGG.sampleMap/LGG_clinicalMatrix"          
#>  [4] "TCGA.KIRP.sampleMap/KIRP_clinicalMatrix"        
#>  [5] "TCGA.CHOL.sampleMap/CHOL_clinicalMatrix"        
#>  [6] "TCGA.COADREAD.sampleMap/COADREAD_clinicalMatrix"
#>  [7] "TCGA.ACC.sampleMap/ACC_clinicalMatrix"          
#>  [8] "TCGA.CESC.sampleMap/CESC_clinicalMatrix"        
#>  [9] "TCGA.READ.sampleMap/READ_clinicalMatrix"        
#> [10] "TCGA.SARC.sampleMap/SARC_clinicalMatrix"        
#> [11] "TCGA.DLBC.sampleMap/DLBC_clinicalMatrix"        
#> [12] "TCGA.PRAD.sampleMap/PRAD_clinicalMatrix"        
#> [13] "TCGA.LUNG.sampleMap/LUNG_clinicalMatrix"        
#> [14] "TCGA.LIHC.sampleMap/LIHC_clinicalMatrix"        
#> [15] "TCGA.KICH.sampleMap/KICH_clinicalMatrix"        
#> [16] "TCGA.HNSC.sampleMap/HNSC_clinicalMatrix"        
#> [17] "TCGA.PCPG.sampleMap/PCPG_clinicalMatrix"        
#> [18] "TCGA.ESCA.sampleMap/ESCA_clinicalMatrix"        
#> [19] "TCGA.THCA.sampleMap/THCA_clinicalMatrix"        
#> [20] "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"        
#> [21] "TCGA.LAML.sampleMap/LAML_clinicalMatrix"        
#> [22] "TCGA.BLCA.sampleMap/BLCA_clinicalMatrix"        
#> [23] "TCGA.SKCM.sampleMap/SKCM_clinicalMatrix"        
#> [24] "TCGA.LUSC.sampleMap/LUSC_clinicalMatrix"        
#> [25] "TCGA.TGCT.sampleMap/TGCT_clinicalMatrix"        
#> [26] "TCGA.PAAD.sampleMap/PAAD_clinicalMatrix"        
#> [27] "TCGA.GBM.sampleMap/GBM_clinicalMatrix"          
#> [28] "TCGA.STAD.sampleMap/STAD_clinicalMatrix"        
#> [29] "TCGA.MESO.sampleMap/MESO_clinicalMatrix"        
#> [30] "TCGA.UVM.sampleMap/UVM_clinicalMatrix"          
#> [31] "TCGA.GBMLGG.sampleMap/GBMLGG_clinicalMatrix"    
#> [32] "TCGA.THYM.sampleMap/THYM_clinicalMatrix"        
#> [33] "TCGA.UCEC.sampleMap/UCEC_clinicalMatrix"        
#> [34] "TCGA.BRCA.sampleMap/BRCA_clinicalMatrix"        
#> [35] "TCGA.UCS.sampleMap/UCS_clinicalMatrix"          
#> [36] "TCGA.COAD.sampleMap/COAD_clinicalMatrix"        
#> [37] "TCGA.FPPP.sampleMap/FPPP_clinicalMatrix"