Error using makeGRangesFromDataFrame in an R workflow for ATAC-seq

Question

[Ethidium Bromide]

New to R. Recently working through an ATAC-seq workshow in R.

In Section 5.1 of where I call the makeGRangesFromDataFrame function I get the following error -

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

I had previously installed the GenomicRanges package and I tried again. No joy. So I attached the package require(GenomicRanges) and now when I receive the following error when I go to repeat the same call -

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

     > 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"

Can anyone tell me what I am doing wrong here?

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

Thanks in advance,

R.

Answer 1

[ATpoint]

Output of packageVersion("GenomicRanges"), head(atac_esca) and class(atac_esca)? Never seen this error message and I use this function like every day. Could be Windows-related or your data frame is in fact not a df but a different class like any of these dplyr formats. I also suggest to never use T/F but always TRUE/FALSE to avoid misinterpretations. And yes, of course you have to load the package first before being able to call functions from it, GenomicRanges is not a base package so you will have to load it at every new session.

[Ethidium Bromide]

Thanks for your reply. edited in the outputs.

[ATpoint]

Can you try again with makeGRangesFromDataFrame(data.frame(atac_esca), keep.extra.columns = TRUE)?

Looks like this is not a standard data frame but a mixture of several other classes.

[Ethidium Bromide]

Thanks!! Well. This certainly produced a different result:

> makeGRangesFromDataFrame(data.frame(atac_esca), keep.extra.columns = TRUE)
GRanges object with 127055 ranges and 5 metadata columns:
           seqnames            ranges strand |        name            score  annotation         percentGC
              <Rle>         <IRanges>  <Rle> | <character>        <numeric> <character>         <numeric>
       [1]     chr1   1290095-1290596      * |    ESCA_107 2.46437811814343      3' UTR 0.676646706586826
       [2]     chr1   1291115-1291616      * |    ESCA_108 2.58792851900195      3' UTR 0.702594810379242
       [3]     chr1   1291753-1292254      * |    ESCA_109 7.57996223017863      3' UTR  0.63872255489022
       [4]     chr1   1440824-1441325      * |    ESCA_160 4.46727398384637      3' UTR 0.658682634730539
       [5]     chr1   1630188-1630689      * |    ESCA_179 20.6213237496952      3' UTR 0.728542914171657
       ...      ...               ...    ... .         ...              ...         ...               ...
  [127051]     chrY 12905438-12905939      * | ESCA_126988 3.60381207684008    Promoter 0.510978043912176
  [127052]     chrY 13479810-13480311      * | ESCA_126990  8.2894261489451    Promoter 0.522954091816367
  [127053]     chrY 19077189-19077690      * | ESCA_126994 2.11891320489898    Promoter 0.620758483033932
  [127054]     chrY 19744492-19744993      * | ESCA_126997 3.99321245552217    Promoter 0.483033932135729
  [127055]     chrY 20575377-20575878      * | ESCA_127001 10.5701261925874    Promoter 0.512974051896208
                   percentAT
                   <numeric>
       [1] 0.323353293413174
       [2] 0.297405189620758
       [3]  0.36127744510978
       [4] 0.341317365269461
       [5] 0.271457085828343
       ...               ...
  [127051] 0.489021956087824
  [127052] 0.477045908183633
  [127053] 0.379241516966068
  [127054] 0.516966067864271
  [127055] 0.487025948103792
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

[Kevin Blighe]

Is that the issue solved, then, EtBr?

[Ethidium Bromide]

Yes, it is. How can I mark this solved for future reference?

[Kevin Blighe]

I have moved this thread to answer, so, feel free to accept the answer.

[ATpoint]

Glad to hear it worked.