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ropensci / UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
https://docs.ropensci.org/UCSCXenaTools
GNU General Public License v3.0
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bad option check in fetch_dense_values #8

Closed ShixiangWang closed 5 years ago

ShixiangWang commented 5 years ago 
> host = "https://toil.xenahubs.net"
> dataset = "tcga_RSEM_gene_tpm"
> samples = c("TCGA-02-0047-01","TCGA-02-0055-01","TCGA-02-2483-01","TCGA-02-2485-01")
> probes = c('ENSG00000282740.1', 'ENSG00000000005.5', 'ENSG00000000419.12')
> genes =c("TP53", "RB1", "PIK3CA")
> fetch_dense_values(host, dataset, genes, samples, check = TRUE, use_probeMap = TRUE)
Checking identifiers...
The following identifiers have been removed fro host https://toil.xenahubs.net dataset tcga_RSEM_gene_tpm
[1] NA NA NA
Done.
Checking samples...
Done.
Checking if the dataset has probeMap...
Done. ProbeMap is found.
Error in dimnames(x) <- dn : 'dimnames'的长度[2]必需与陈列范围相等