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, ... )
x | a XenaHub object |
---|---|
filterCohorts | default is |
filterDatasets | default is |
ignore.case | if |
... | other arguments except |
a XenaHub
object
Shixiang Wang [email protected]
#> 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#> [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"