I get an error, not sure what's wrong there... Hope the authors of the package can make the error message more informative.
requireUniProt.ws)
up <- UniProt.ws(taxId=9606)
res <- select(up,
keytype = "UNIPROTKB",
keys = c('Q9NTX7', 'P19484', 'Q6ZSR9', 'A6NKZ8'),
columns = c('ENTREZ_GENE', 'GENES', 'GENEID')
)
#
# Error in .resortColumns(tab, jointype, reqCols) :
# [internal] some of 'reqCols' are not in 'tab'
# In addition: Warning message:
# In `[<-.factor`(`*tmp*`, iseq, value = c("Q9NTX7", "P19484", "Q6ZSR9", :
# invalid factor level, NA generated
UPD. adding sessionInfo()
:
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] UniProt.ws_2.26.0 BiocGenerics_0.32.0 RCurl_1.98-1.2 RSQLite_2.2.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 rstudioapi_0.11 AnnotationDbi_1.48.0 magrittr_1.5 rappdirs_0.3.1
[6] IRanges_2.20.2 tidyselect_1.1.0 bit_4.0.4 R6_2.4.1 rlang_0.4.7
[11] httr_1.4.2 dplyr_1.0.1 blob_1.2.1 tools_3.6.1 Biobase_2.46.0
[16] DBI_1.1.0 dbplyr_1.4.4 ellipsis_0.3.0 assertthat_0.2.1 bit64_4.0.2
[21] digest_0.6.25 tibble_3.0.1 lifecycle_0.2.0 crayon_1.3.4 purrr_0.3.4
[26] vctrs_0.3.2 S4Vectors_0.24.4 bitops_1.0-6 curl_4.3 glue_1.4.0
[31] memoise_1.1.0 BiocFileCache_1.10.2 compiler_3.6.1 pillar_1.4.6 generics_0.0.2
[36] stats4_3.6.1 pkgconfig_2.0.3
Would you be able to provide the output of
sessionInfo()
for this?added sessionInfo().
Can you please provide your
sessionInfo()
I can not currently reproduce thisadded sessionInfo() (should have provided it from the very beginning, sorry)