r - 在 ATAC-seq 的 R 工作流程中使用 makeGRangesFromDataFrame 时出错

Question

R 新手。最近正在研究 ATAC-seq workshow in R 。

在第 5.1 节中，我调用 makeGRangesFromDataFrame 函数，出现以下错误 -

> atac_esca.gr <- makeGRangesFromDataFrame(atac_esca,keep.extra.columns = T)
Error in makeGRangesFromDataFrame(atac_esca, keep.extra.columns = T) : could not find function "makeGRangesFromDataFrame"

我之前安装了 GenomicRanges 软件包，并再次尝试。没有喜悦。所以我附上了包 require(GenomicRanges) 现在，当我重复相同的调用时收到以下错误 -

> atac_esca.gr <- makeGRangesFromDataFrame(atac_esca,keep.extra.columns = T)
Error in inherits(object, class2) : 'what' must be a character vector

[编辑]:输出结果

> dput(head(atac_esca,10))
structure(list(seqnames = c("chr1", "chr1", "chr1", "chr1", "chr1", 
"chr1", "chr1", "chr1", "chr1", "chr1"), start = c(1290095, 1291115, 
1291753, 1440824, 1630188, 2030218, 2184484, 2185113, 2185905, 
2186860), end = c(1290596, 1291616, 1292254, 1441325, 1630689, 
2030719, 2184985, 2185614, 2186406, 2187361), name = c("ESCA_107", 
"ESCA_108", "ESCA_109", "ESCA_160", "ESCA_179", "ESCA_341", "ESCA_539", 
"ESCA_540", "ESCA_541", "ESCA_542"), score = c(2.46437811814343, 
2.58792851900195, 7.57996223017863, 4.46727398384637, 20.6213237496952, 
15.5725811237533, 19.2854359599157, 11.1907656456091, 22.2148888990001, 
22.8844119795596), annotation = c("3' UTR", "3' UTR", "3' UTR", 
"3' UTR", "3' UTR", "3' UTR", "3' UTR", "3' UTR", "3' UTR", "3' UTR"
), percentGC = c(0.676646706586826, 0.702594810379242, 0.63872255489022, 
0.658682634730539, 0.728542914171657, 0.6187624750499, 0.578842315369261, 
0.604790419161677, 0.63872255489022, 0.439121756487026), percentAT = c(0.323353293413174, 
0.297405189620758, 0.36127744510978, 0.341317365269461, 0.271457085828343, 
0.3812375249501, 0.421157684630739, 0.395209580838323, 0.36127744510978, 
0.560878243512974)), spec = structure(list(cols = list(seqnames = structure(list(), class = c("collector_character", 
"collector")), start = structure(list(), class = c("collector_double", 
"collector")), end = structure(list(), class = c("collector_double", 
"collector")), name = structure(list(), class = c("collector_character", 
"collector")), score = structure(list(), class = c("collector_double", 
"collector")), annotation = structure(list(), class = c("collector_character", 
"collector")), percentGC = structure(list(), class = c("collector_double", 
"collector")), percentAT = structure(list(), class = c("collector_double", 
"collector"))), default = structure(list(), class = c("collector_guess", 
"collector")), skip = 1), class = "col_spec"), row.names = c(NA, 
10L), class = c("spec_tbl_df", "tbl_df", "tbl", "data.frame"))

> head (atac_esca)
  seqnames   start     end     name     score annotation percentGC percentAT
1     chr1 1290095 1290596 ESCA_107  2.464378     3' UTR 0.6766467 0.3233533
2     chr1 1291115 1291616 ESCA_108  2.587929     3' UTR 0.7025948 0.2974052
3     chr1 1291753 1292254 ESCA_109  7.579962     3' UTR 0.6387226 0.3612774
4     chr1 1440824 1441325 ESCA_160  4.467274     3' UTR 0.6586826 0.3413174
5     chr1 1630188 1630689 ESCA_179 20.621324     3' UTR 0.7285429 0.2714571
6     chr1 2030218 2030719 ESCA_341 15.572581     3' UTR 0.6187625 0.3812375

> packageVersion("GenomicRanges")
[1] ‘1.38.0’

> class(atac_esca)
[1] "spec_tbl_df" "tbl_df"      "tbl"         "data.frame"

谁能告诉我我在这里做错了什么？

[使用 R Studio 1.2.5033 - R 3.6.3 - Windows 10]

提前致谢，

R。

Answer 1

您有一个 tibble，并且函数 makeGRangesFromDataFrame 与 data.frame 一起使用。处理额外的列时会引发一些问题:

str(atac_esca)
Classes ‘spec_tbl_df’, ‘tbl_df’, ‘tbl’ and 'data.frame':    10 obs. of  8 variables:
 $ seqnames  : chr  "chr1" "chr1" "chr1" "chr1" ...
 $ start     : num  1290095 1291115 1291753 1440824 1630188 ...
 $ end       : num  1290596 1291616 1292254 1441325 1630689 ...
 $ name      : chr  "ESCA_107" "ESCA_108" "ESCA_109" "ESCA_160" ...
 $ score     : num  2.46 2.59 7.58 4.47 20.62 ...
 $ annotation: chr  "3' UTR" "3' UTR" "3' UTR" "3' UTR" ...
 $ percentGC : num  0.677 0.703 0.639 0.659 0.729 ...
 $ percentAT : num  0.323 0.297 0.361 0.341 0.271 ...
 - attr(*, "spec")=List of 3
  ..$ cols   :List of 8
  .. ..$ seqnames  : list()
  .. .. ..- attr(*, "class")= chr  "collector_character" "collector"
  .. ..$ start     : list()
  .. .. ..- attr(*, "class")= chr  "collector_double" "collector"

这有效:

 makeGRangesFromDataFrame(atac_esca)
GRanges object with 10 ranges and 0 metadata columns:
       seqnames          ranges strand
          <Rle>       <IRanges>  <Rle>
   [1]     chr1 1290095-1290596      *
   [2]     chr1 1291115-1291616      *
   [3]     chr1 1291753-1292254      *

要保留其他列，您需要转换为 data.frame:

makeGRangesFromDataFrame(as.data.frame(atac_esca),keep.extra.columns = TRUE)
GRanges object with 10 ranges and 5 metadata columns:
       seqnames          ranges strand |        name            score
          <Rle>       <IRanges>  <Rle> | <character>        <numeric>
   [1]     chr1 1290095-1290596      * |    ESCA_107 2.46437811814343
   [2]     chr1 1291115-1291616      * |    ESCA_108 2.58792851900195
   [3]     chr1 1291753-1292254      * |    ESCA_109 7.57996223017863
   [4]     chr1 1440824-1441325      * |    ESCA_160 4.46727398384637