Hello,
I have bedgraph files in following format:
track type=bedGraph description=center_label visibility=full graphType=points color=200,100,0 altColor=0,100,200
chr1 923391 923526 -0.4838883
chr1 924813 925002 -0.45778788
chr1 930090 930401 -0.09189046
chr1 935707 935961 1.25254348
chr1 939207 939525 3.51303879
Is there any tool, with whom I can convert bedgraph to Granges object? Desired format is something like this:
> grl.data
GRangesList object of length 10:
$s1
GRanges object with 1318 ranges and 1 metadata column:
seqnames ranges strand | value
<Rle> <IRanges> <Rle> | <numeric>
[1] 1 1-576 * | 2.03030
[2] 1 577-1112 * | 1.94532
[3] 1 1113-1511 * | 1.92982
[4] 1 1512-2113 * | 1.86865
[5] 1 2114-2573 * | 1.93882
... ... ... ... . ...
[1314] 22 19081-19153 * | 2.00131
[1315] 22 19154-20059 * | 1.95003
[1316] 22 20060-21926 * | 2.00952
[1317] 22 21927-23554 * | 1.95225
[1318] 22 23555-24465 * | 2.01210
Currently I was not able to find any related solution, so will be happy for any help
Thank you!
•
written
by
storm1907 •
the import function from rtracklayer
I work on remote Linux server, and have difficulties with installing and running rtracklayer. Will try to do it on my local machine, thanks
If you don't want to install rtracklayer you could also build the GRanges semi-manually.
library("GenomicRanges")
bg <- read.table("file.bedgraph", sep="\t", skip=1)
colnames(bg) <- c("seqnames", "start", "end", "value")
gr <- makeGRangesFromDataFrame(bg, ignore.strand=TRUE, keep.extra.columns=TRUE)
Thank you, this works for one sample! What could be appropriate approach, if I need to make one Grange list object from multiple bedgraphs?
library("GenomicRanges")
# A vector of bedGraph files.
# Can be constructed with list.files for convenience.
bg_files <- c("file1.bedgraph", "file2.bedgrah")
# Load the bedgraphs files into a list of GRanges.
bgs <- lapply(bg_files, function(x) {
bg <- read.table(x, sep="\t", skip=1)
colnames(bg) <- c("seqnames", "start", "end", "value")
gr <- makeGRangesFromDataFrame(bg, ignore.strand=TRUE, keep.extra.columns=TRUE)
return(gr)
})
# Convert the list of GRanges into a GRangesList.
gr_list <- GRangesList(bgs)
Thank you!
At first it is working, however when trying to run R package CINdex, I still get error
> gr_list
GRangesList object of length 4:
[[1]]
GRanges object with 200255 ranges and 1 metadata column:
seqnames ranges strand | value
<Rle> <IRanges> <Rle> | <numeric>
[1] chr1 923391-923526 * | 0.544787
[2] chr1 923551-924817 * | 0.565173
[3] chr1 924813-925002 * | 1.072250
[4] chr1 925877-926078 * | -0.511750
[5] chr1 930090-930401 * | 0.270485
... ... ... ... . ...
[200251] chr22 50768711-50768939 * | 1.2515725
[200252] chr22 50769840-50770081 * | 0.2780226
[200253] chr22 50775707-50775916 * | 0.0372048
[200254] chr22 50776605-50776814 * | -0.2125530
[200255] chr22 50777887-50778046 * | 0.3990656
-------
seqinfo: 22 sequences from an unspecified genome; no seqlengths
...
<3 more elements>
> run.cin.chr(gr_list)
Error in segments.to.profile(segments) :
Wrong representation of segments.
In addition: Warning message:
In dir.create(out.folder.name) : 'output_chr_cin' already exists
Hello again,
This is the result of my commands (my_gr). However, is it possible to get result as in the lower sample (grl.data)?
in grl.data file start there are two additional lines:
GRangesList object of length 10:
$s1
When I try to run downstream analysis, everything is ok with file grl.data, but for my_gr I get output:
> run.cin.chr(grl.seg = ivf_gr)
Error in run.cin.chr(grl.seg = ivf_gr) :
Input 'grl.seg' must be a GRangesList object
grl.data is a sample file, provided by CINdex package
•
written
by
storm1907 •
OK, I found this function for making Grange lists: https://rdrr.io/bioc/GenomicRanges/man/makeGRangesListFromDataFrame.html
However, still the question, how to make one Grange object list from multiple bedgraphs
I also tried to make Granges list object from 1 bedgraph file
Trying to run analysis with this new file I got following error:
> run.cin.chr(grl.seg = ivf_gr1)
Error in segments.to.profile(segments) :
Wrong representation of segments.
In addition: Warning message:
In dir.create(out.folder.name) : 'output_chr_cin' already exists
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