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waldronlab / cBioPortalData

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
https://waldronlab.io/cBioPortalData/
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geneTable() #29

Closed xinwei-sher closed 4 years ago

xinwei-sher commented 4 years ago

geneTable() returns exactly 100,000 genes. Is that all? Why most of the genes from geneTable() are phosphoprotein, and there are only 3477 protein-coding genes?

geneTable(cbio) %>% group_by(type) %>% summarise(n=n())

A tibble: 9 x 2

type n

1 miRNA 3925 2 ncRNA 6 3 other 158 4 phosphoprotein 91907 5 protein-coding 3477 6 pseudo 291 7 rRNA 2 8 tRNA 22 9 unknown 212 Such as, 95817 | CCDC61_PT285 | phosphoprotein | NA | NA | NA -- | -- | -- | -- | -- | -- 20 | -95816 | CCDC61_PS447 | phosphoprotein | NA | NA | NA 21 | -95815 | FCGBP_PY614 | phosphoprotein | NA | NA | NA 22 | -95814 | FCGBP_PT624 | phosphoprotein | NA | NA | NA Even TP53 is not there: > geneTable(cbio) %>% filter(hugoGeneSymbol=="TP53") # A tibble: 0 x 6 # ... with 6 variables: entrezGeneId , hugoGeneSymbol , type , cytoband , length , chromosome Warning message: `...` is not empty. How come?
LiNk-NY commented 4 years ago

@xinwei-sher Thanks for reporting the issue. I am preparing a patch. There are pagination parameters in the API that are not explicit in the function arguments.