: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/
Error in auto_copy():
! x and y must share the same src.
ℹ x is a <tbl_df/tbl/data.frame> object.
ℹ y is a list.
ℹ Set copy = TRUE if y can be copied to the same source as x (may be slow).
Run rlang::last_trace() to see where the error occurred.
I think this is due to the fact that cli is not a 6 x 157 nibble as in your markdown, but rather a list of 2 tibbles ($LUAD_clinicalMatrix # and $LUAD_survival.txt), each containing part of the needed info. Any suggestions? Thanks!
Hi, I tried to use the markdown published on https://ropensci.org/blog/2019/09/06/ucscxenatools-surv/
This is what happens:
merged_data = tibble(sampleID = names(KRAS), KRAS_expression = as.numeric(KRAS)) %>% left_join(cli, by = "sampleID") %>% filter(sample_type == "Primary Tumor") %>% # Keep only 'Primary Tumor' select(sampleID, KRAS_expression, OS.time, OS) %>% rename(time = OS.time, status = OS)
Error in
auto_copy()
: !x
andy
must share the same src. ℹx
is a <tbl_df/tbl/data.frame> object. ℹy
is a list. ℹ Setcopy = TRUE
ify
can be copied to the same source asx
(may be slow). Runrlang::last_trace()
to see where the error occurred.I think this is due to the fact that cli is not a 6 x 157 nibble as in your markdown, but rather a list of 2 tibbles ($LUAD_clinicalMatrix # and $LUAD_survival.txt), each containing part of the needed info. Any suggestions? Thanks!