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40 運行GDCprepare(query, save=FALSE)時錯誤

運行prepare的時候提示column有問題
下面是我運行的代碼
有什么解決辦法么

> 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)


在運行下面這一步時提示error,是不是因為最早sampleDown時只取了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(...)

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1 個回答

omicsgene - 生物信息
擅長:重測序,遺傳進化,轉錄組,GWAS

建議 下載所有的數據過后,再通過sample.info 信息篩選表達表格,避免錯誤:

看看這個:

http://gollyjoe.com/article/1664?

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