UCSCXenaTools: Retrieve Gene Expression and Clinical Information from UCSC Xena for Survival Analysis

[gbregni]

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 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!

[github-actions]

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

[ShixiangWang]

Sorry for the delay. The data source has been changed.

cli = XenaPrepare(cli_query)

cli$LUAD_clinicalMatrix
cli$LUAD_survival.txt

You have to merged the two dataframe as a dataframe.