GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment

Question

[Antonia]

I am trying to get the combined peaks from a list of objects in atac data and I am running into the following error.

GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment

My code is

combined.peaks <- reduce(c(peaks$sample1, peaks$sample2,
                           peaks$sample3, peaks$sample4
                           ))

This was working a few days ago btw... Is this a new bug?

Thanks!

T

[Ming Tommy Tang]

Use GenomicRanges::reduce()

[ATpoint]

Please add a reproducible example via dput.

[Antonia]

inputFiles <- c("./sample1/outs/fragments.tsv.gz", "./sample2/outs/fragments.tsv.gz", "./sample3/outs/fragments.tsv.gz", "./sample4/outs/fragments.tsv.gz")'

names(inputFiles) = c("sample1", "sample2", "sample3", "sample4") barcodes = list() peaks = GRangesList()

for(i in names(matrixFiles)){ barcodes[[i]] = as.data.frame(readr::read_tsv(file = paste0(matrixFiles[i],"filtered_peak_bc_matrix/barcodes.tsv")), col_names = F)[,1] p = as.data.frame(readr::read_tsv(file = paste0(matrixFiles[i],"filtered_peak_bc_matrix/peaks.bed")), col_names = F)[,1:3] colnames(p) = c("chr","start","end") peaks[[i]] = makeGRangesFromDataFrame(df = p) }

combined.peaks <- reduce(c(peaks$sample1, peaks$sample2, peaks$sample3, peaks$sample4 ))

[Ram]

This is obviously not reproducible for anyone that does not have your fragments.tsv.gz files. Please follow ATPoint's advice and use dput on objects.

[ATpoint]

We still do not know how exactly your GRanges objects look, that is why I asked for dput.

This works:

gr0 <- GRanges(Rle(c("chr2", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
               IRanges(1:10, width=10:1))

gr1 <- gr0
gr2 <- gr0

reduce(c(gr0, gr1, gr2))

so if you need help provide data (not code, and not as a screenshot)

[Antonia]

I am sorry for that. This is what my object looks like. Is this more useful to you for providing a solution?

peaks
GRangesList object of length 11:
$sample1
GRanges object with 98860 ranges and 0 metadata columns:
          seqnames            ranges strand
             <Rle>         <IRanges>  <Rle>
      [1]     chr1     629770-630550      *
      [2]     chr1     633794-634259      *
      [3]     chr1     778203-779262      *
      [4]     chr1     817083-817625      *
      [5]     chr1     821110-821501      *
      ...      ...               ...    ...
  [98856]     chrY 56868863-56871397      *
  [98857]     chrY 56872276-56872281      *
  [98858]     chrY 56873716-56874522      *
  [98859]     chrY 56877566-56877837      *
  [98860]     chrY 56879680-56880015      *
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

...
<10 more elements>

[ATpoint]

Please show the output of

dput(sapply(peaks, function(x) head(x, 2), simplify=FALSE))

[Antonia]

list(AML5226 = new("GRanges", seqnames = new("Rle", values = structure(1L, levels = c("chr1", 
"chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", 
"chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", 
"chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", 
"chrY"), class = "factor"), lengths = 2L, elementMetadata = NULL, 
    metadata = list()), ranges = new("IRanges", start = c(629770L, 
633794L), width = c(781L, 466L), NAMES = NULL, elementType = "ANY", 
    elementMetadata = NULL, metadata = list()), strand = new("Rle", 
    values = structure(3L, levels = c("+", "-", "*"), class = "factor"), 
    lengths = 2L, elementMetadata = NULL, metadata = list()), 
    seqinfo = new("Seqinfo", seqnames = c("chr1", "chr2", "chr3", 
    "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", 
    "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", 
    "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"
    ), seqlengths = c(NA_integer_, NA_integer_, NA_integer_, 
    NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, 
    NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, 
    NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, 
    NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, 
    NA_integer_), is_circular = c(NA, NA, NA, NA, NA, NA, NA, 
    NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
    NA, NA), genome = c(NA_character_, NA_character_, NA_character_, 
    NA_character_, NA_character_, NA_character_, NA_character_, 
    NA_character_, NA_character_, NA_character_, NA_character_, 
    NA_character_, NA_character_, NA_character_, NA_character_, 
    NA_character_, NA_character_, NA_character_, NA_character_, 
    NA_character_, NA_character_, NA_character_, NA_character_, 
    NA_character_)), elementMetadata = new("DFrame", rownames = NULL, 
        nrows = 2L, elementType = "ANY", elementMetadata = NULL, 
        metadata = list(), listData = structure(list(), names = character(0))), 
    elementType = "ANY", metadata = list()),

[ATpoint]

It's incomplete. Without a reproducible this thread is pointless.

[Antonia]

This is a long output and it's not accepted by biostars to be posted. Can I send this to you via email?

[Ram]

Use a Gist when content is too large for Biostars

Answer 1

[benformatics]

Something is probably wrong with your files and one of the entries is not a GRanges object

combined.peaks <- reduce(unlist(GRangesList(c(peaks$sample1, peaks$sample2,peaks$sample3, peaks$sample4))))

You probably need to provide the head() of the peaks$sample1 etc...for us to be certain

Note: You may need to use GenomicRanges::reduce() if you have other packages loaded and get an error about lists

[Antonia]

This was working on Friday, it is not working now. So, I don't think this is related to my data, but rather something to GRanges.

[Ram]

Did you update R?

[Antonia]

No, nothing should have been changed.

[benformatics]

Something has changed...

what does lapply(peaks,length) give you?

[Antonia]

lapply(peaks,length)
$sample1
[1] 98860

$sample2
[1] 76862

$sample3
[1] 120326

$sample4
[1] 85919

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.

[benformatics]

What happens if you do like:

reduce(c(peaks$sample1,peaks$sample2))

and like the same for 1 and 3 and 1 and 4... etc.. Do they all fail with the same error or do some work?

[Antonia]

yes, any combo of those fails.

[benformatics]

Your peaks object is probably a GRanges instead of a GRangesList.

What about trying to set:

peaks <- GRangesList(peaks)

Does the error change?

[Antonia]

I have set this up already.

[Amitm]

Hi,

Were you able to resolve this? I had the same error message and a google search landed me here. So, posting what I think was the reason in my case at least -

## example GRanges object
summary(my.sel.peaks.gr)
# [1] "GRanges object with 7536 ranges and 0 metadata columns"
##
library(tidyverse)
## Among other msgs of conflicts
# purrr::reduce()       masks GenomicRanges::reduce(), IRanges::reduce()
##
## So -
reduce(my.sel.peaks.gr)
# Error in getListElement(x, i, ...) : 
#   GRanges objects don't support [[, as.list(), lapply(), or unlist() at
#   the moment
##
## But -
GenomicRanges::reduce(my.sel.peaks.gr)
# GRanges object with 7269 ranges and 0 metadata columns:
#          seqnames            ranges strand
#             <Rle>         <IRanges>  <Rle>
#      [1]     chr1     629793-630083      *
#      [2]     chr1     632733-633039      *
#      [3]     chr1     633868-634183      *
#      ...      ...               ...    ...
#   [7269]     chrY 19567023-19567392      *
#   -------
#   seqinfo: 24 sequences from an unspecified genome; no seqlengths
##

So, explicitly specifying the package from where I wanted to use reduce from, resolved the issue. Selected session info -

R version 4.2.0 (2022-04-22)
GenomicRanges_1.50.0
tidyverse_2.0.0
purrr_1.0.1

[new]

I had the same issue: your fix worked for me too - thanks!