Error in fetch_dense_values

[jbagnot]

Hello, thank you for the wonderful tool. First time posting, so please let me know if this issue has been solved elsewhere (I couldn't find) or if more information would be helpful. I have been using a method similar to that outlined here (https://shixiangwang.github.io/home/en/post/ucscxenatools-201908/) for fetching dense values for quite some time, but at some point the past few months my previous code started throwing the following error message when running: Error in FUN(X[[i]], ...) : is.atomic(p) | is.list(p) is not TRUE

I get it running the same code as the vignette:

> luad_cohort = XenaData %>%
+     filter(XenaHostNames == "tcgaHub") %>% # select TCGA Hub
+     XenaScan("TCGA Lung Adenocarcinoma")   # select LUAD cohort
> luad_cohort
# A tibble: 23 × 17
   XenaHosts                XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label Type 
   <chr>                    <chr>         <chr>       <chr>              <int> <chr>       <chr> <chr>
 1 https://tcga.xenahubs.n… tcgaHub       TCGA Lung … RABIT/separ…         467 pathway ac… RABI… clin…
 2 https://tcga.xenahubs.n… tcgaHub       TCGA Lung … RABIT/separ…         120 pathway ac… RABI… clin…
 3 https://tcga.xenahubs.n… tcgaHub       TCGA Lung … TCGA.LUAD.s…         151 DNA methyl… Meth… geno…
 4 https://tcga.xenahubs.n… tcgaHub       TCGA Lung … TCGA.LUAD.s…         492 DNA methyl… Meth… geno…

> ge <- luad_cohort %>%
+     filter(DataSubtype == 'gene expression RNAseq', Label == 'IlluminaHiSeq')
> ge
# A tibble: 1 × 17
  XenaHosts                 XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label Type 
  <chr>                     <chr>         <chr>       <chr>              <int> <chr>       <chr> <chr>
1 https://tcga.xenahubs.net tcgaHub       TCGA Lung … TCGA.LUAD.s…         576 gene expre… Illu… geno…
# ℹ 9 more variables: AnatomicalOrigin <chr>, SampleType <chr>, Tags <chr>, ProbeMap <chr>,
#   LongTitle <chr>, Citation <chr>, Version <chr>, Unit <chr>, Platform <chr>

> KRAS = fetch_dense_values(host = ge$XenaHosts,
+                           dataset = ge$XenaDatasets,
+                           identifiers = "KRAS",
+                           use_probeMap = TRUE) %>%
+     .[1, ]
Error in FUN(X[[i]], ...) : is.atomic(p) | is.list(p) is not TRUE

[github-actions]

Thanks for reporting, Shixiang will reply as soon as possible:)

[ShixiangWang]

Should be networking issue.

> library(UCSCXenaTools)
> luad_cohort = XenaData %>%
+   dplyr::filter(XenaHostNames == "tcgaHub") %>% # select TCGA Hub
+   XenaScan("TCGA Lung Adenocarcinoma")   # select LUAD cohort
> luad_cohort
# A tibble: 23 × 17
   XenaHosts    XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype
   <chr>        <chr>         <chr>       <chr>              <int> <chr>      
 1 https://tcg… tcgaHub       TCGA Lung … RABIT/separ…         467 pathway ac…
 2 https://tcg… tcgaHub       TCGA Lung … RABIT/separ…         120 pathway ac…
 3 https://tcg… tcgaHub       TCGA Lung … TCGA.LUAD.s…         151 DNA methyl…
 4 https://tcg… tcgaHub       TCGA Lung … TCGA.LUAD.s…         492 DNA methyl…
 5 https://tcg… tcgaHub       TCGA Lung … TCGA.LUAD.s…         516 copy numbe…
 6 https://tcg… tcgaHub       TCGA Lung … TCGA.LUAD.s…         237 protein ex…
 7 https://tcg… tcgaHub       TCGA Lung … TCGA.LUAD.s…         576 gene expre…
 8 https://tcg… tcgaHub       TCGA Lung … TCGA.LUAD.s…          60 miRNA matu…
 9 https://tcg… tcgaHub       TCGA Lung … TCGA.LUAD.s…         576 gene expre…
10 https://tcg… tcgaHub       TCGA Lung … TCGA.LUAD.s…         576 gene expre…
# ℹ 13 more rows
# ℹ 11 more variables: Label <chr>, Type <chr>, AnatomicalOrigin <chr>,
#   SampleType <chr>, Tags <chr>, ProbeMap <chr>, LongTitle <chr>,
#   Citation <chr>, Version <chr>, Unit <chr>, Platform <chr>
# ℹ Use `print(n = ...)` to see more rows
> ge <- luad_cohort %>%
+   dplyr::filter(DataSubtype == 'gene expression RNAseq', Label == 'IlluminaHiSeq')
> ge
# A tibble: 1 × 17
  XenaHosts     XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype
  <chr>         <chr>         <chr>       <chr>              <int> <chr>      
1 https://tcga… tcgaHub       TCGA Lung … TCGA.LUAD.s…         576 gene expre…
# ℹ 11 more variables: Label <chr>, Type <chr>, AnatomicalOrigin <chr>,
#   SampleType <chr>, Tags <chr>, ProbeMap <chr>, LongTitle <chr>,
#   Citation <chr>, Version <chr>, Unit <chr>, Platform <chr>
> KRAS = fetch_dense_values(host = ge$XenaHosts,
+                           dataset = ge$XenaDatasets,
+                           identifiers = "KRAS",
+                           use_probeMap = TRUE) %>%
+   .[1, ]
-> Obtaining gene symbols from probeMap...
-> Checking identifiers...
-> Done.
-> Checking samples...
-> Done.
-> Checking if the dataset has probeMap...
-> Done. ProbeMap is found.
> KRAS
TCGA-69-7978-01 TCGA-62-8399-01 TCGA-78-7539-01 TCGA-50-5931-11 
         10.250          10.290          10.820          10.290 

[jbagnot]

Thank you for the reply. I'm not sure what was causing the error exactly, but I found a work around in which I set samples equal to the 'sample' column from the clinical query survival object. For some reason I get this error when samples = NULL. Using the vignette the following then was successful:

KRAS = fetch_dense_values(host = ge$XenaHosts,
+                           dataset = ge$XenaDatasets,
+                           identifiers = "KRAS",
+                           samples = cli$LUAD_survival.txt$sample,
+                           use_probeMap = TRUE) %>%
+   .[1, ]