运行prepare的时候提示column有问题
下面是我运行的代码
有什么解决办法么
> query <- GDCquery(project = "TCGA-BRCA",
+ data.category = "Transcriptome Profiling",
+ data.type = "Gene Expression Quantification",
+ workflow.type = "STAR - Counts")
> queryFt <- GDCquery(project = "TCGA-BRCA",
+ data.category = "Transcriptome Profiling",
+ data.type = "Gene Expression Quantification",
+ workflow.type = "STAR - Counts")
> samplesDown <- getResults(queryFt,cols=c("cases"))
> dataSmTP <- TCGAquery_SampleTypes(barcode = samplesDown,
+ typesample = "TP")
> dataSmNT <- TCGAquery_SampleTypes(barcode = samplesDown,
+ typesample = "NT")
> dataSmTP_short <- dataSmTP[1:100]
> dataSmNT_short <- dataSmNT[1:100]
> queryDownSd <- GDCquery(project = "TCGA-BRCA",
+ data.category = "Transcriptome Profiling",
+ data.type = "Gene Expression Quantification",
+ workflow.type = "STAR - Counts",
+ barcode = c(dataSmTP_short, dataSmNT_short))
> GDCdownload(query = queryDownSd, files.per.chunk = 10)
在运行下面这一步时提示error，是不是因为最早sampleDown时只取了case？
> dataPrep1 <- GDCprepare(query = queryDownSd, save = FALSE)
Error in `vectbl_as_col_location()`:
! Can't subset columns past the end.
i Locations 2, 3, and 4 don't exist.
i There is only 1 column.
Run `rlang::last_error()` to see where the error occurred.
There were 50 or more warnings (use warnings() to see the first 50)
> rlang::last_error()
<error/vctrs_error_subscript_oob>
Error in `vectbl_as_col_location()`:
! Can't subset columns past the end.
i Locations 2, 3, and 4 don't exist.
i There is only 1 column.
---
Backtrace:
1. TCGAbiolinks::GDCprepare(query = queryDownSd, save = FALSE)
6. purrr::map_dfc(., .f = function(y) y[, 2:4])
7. purrr::map(.x, .f, ...)
8. TCGAbiolinks .f(.x[[i]], ...)
12. tibble:::`[.tbl_df`(y, , 2:4)
13. tibble:::vectbl_as_col_location(...)
Run `rlang::last_trace()` to see the full context.
> rlang::last_trace()
<error/vctrs_error_subscript_oob>
Error in `vectbl_as_col_location()`:
! Can't subset columns past the end.
i Locations 2, 3, and 4 don't exist.
i There is only 1 column.
---
Backtrace:
x
1. +-TCGAbiolinks::GDCprepare(query = queryDownSd, save = FALSE)
2. | \-TCGAbiolinks:::readTranscriptomeProfiling(...)
3. | +-base::suppressMessages(...)
4. | | \-base::withCallingHandlers(...)
5. | \-x %>% map_dfc(.f = function(y) y[, 2:4])
6. \-purrr::map_dfc(., .f = function(y) y[, 2:4])
7. \-purrr::map(.x, .f, ...)
8. \-TCGAbiolinks .f(.x[[i]], ...)
9. +-y[, 2:4]
10. +-readr:::`[.spec_tbl_df`(y, , 2:4)
11. +-base::NextMethod(`[`)
12. \-tibble:::`[.tbl_df`(y, , 2:4)
13. \-tibble:::vectbl_as_col_location(...)
14. +-tibble:::subclass_col_index_errors(...)
15. | \-base::withCallingHandlers(...)
16. \-vctrs::vec_as_location(j, n, names)
17. \-vctrs `<fn>`()
18. \-vctrs:::stop_subscript_oob(...)
19. \-vctrs:::stop_subscript(...)
20. \-rlang::abort(...)
