Unable to obtain SIGNAL_VALUE for bedgraph files in DeepBlueR
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@helimelanie-15780
Last seen 4.6 years ago

 

Hi, 

I am using DeepBlueR trying to get several tracks from the CEEHRC project's epigenomics data (signal value) for a single gene (GJA1). The files are in bedgraph format. I can't get the value for any bedgraph (or wig file, be it for CEEHRC or Roadmap Epigenomics). However I can get the peak data (bed files). Did I missed something? I could not even find the word begraph in the DeepBlueR user guide but I took the experiment name on DeepBlue online experiment grid. So I assumed I could read it with DeepBlueR...

 

library(DeepBlueR)
query_id <- deepblue_select_experiments(
experiment_name= c("A35262.H3K27ac.merge_bwa.hg19a.A35262_2_lanes_dupsFlagged.q5.F1028.PET.ucsc.bedgraph"),
          chromosome="chr6", 
          start=121756745, 
          end=121770872)
request_id <- deepblue_get_regions(query_id=query_id,                                            output_format="CHROMOSOME,START,END,SIGNAL_VALUE,PEAK,@BIOSOURCE,@PROJECT")
regions <- deepblue_download_request_data(request_id=request_id)
regions

 I can access the file but the SIGNAL_VALUE field is empty...

GRanges object with 472 ranges and 4 metadata columns:
        seqnames                 ranges strand | SIGNAL_VALUE      PEAK  @BIOSOURCE    @PROJECT
           <Rle>              <IRanges>  <Rle> |  <character> <integer> <character> <character>
    [1]     chr6 [121756609, 121756779]      * |                   <NA>      breast      CEEHRC
    [2]     chr6 [121756779, 121756813]      * |                   <NA>      breast      CEEHRC
    [3]     chr6 [121756813, 121756872]      * |                   <NA>      breast      CEEHRC
    [4]     chr6 [121756872, 121756899]      * |                   <NA>      breast      CEEHRC
    [5]     chr6 [121756899, 121756916]      * |                   <NA>      breast      CEEHRC
    ...      ...                    ...    ... .          ...       ...         ...         ...
  [468]     chr6 [121770753, 121770805]      * |                   <NA>      breast      CEEHRC
  [469]     chr6 [121770805, 121770857]      * |                   <NA>      breast      CEEHRC
  [470]     chr6 [121770857, 121770860]      * |                   <NA>      breast      CEEHRC
  [471]     chr6 [121770860, 121770863]      * |                   <NA>      breast      CEEHRC
  [472]     chr6 [121770863, 121770881]      * |                   <NA>      breast      CEEHRC
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

 

Thanks a lot for your help!

 

 

 

 

 

 

 
deepbluer CEEHRC debgraph • 677 views
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Entering edit mode
Markus List ▴ 20
@markus-list-8762
Last seen 3.9 years ago
Freising

Hi,

You don't find any signal values because you request data from a non-existing column. You can get a preview of the file you are interested in the web interface 

http://deepblue.mpi-inf.mpg.de/dashboard.php#ajax/deepblue_view_experiments.php

 

or via 

deepblue_preview_experiment("A35262.H3K27ac.merge_bwa.hg19a.A35262_2_lanes_dupsFlagged.q5.F1028.PET.ucsc.bedgraph")
Called method: deepblue_preview_experiment
Reported status was: okay
[1] "CHROMOSOME\tSTART\tEND\tVALUE\n

As you can see the signal value column is called VALUE, thus modifying your code slightly solves the issue:

> request_id <- deepblue_get_regions(query_id=query_id,                                            output_format="CHROMOSOME,START,END,VALUE,@BIOSOURCE,@PROJECT")
GRanges object with 472 ranges and 3 metadata columns:
        seqnames                 ranges strand |       VALUE  @BIOSOURCE    @PROJECT
           <Rle>              <IRanges>  <Rle> | <character> <character> <character>
    [1]     chr6 [121756609, 121756779]      * |      5.0000      breast      CEEHRC
    [2]     chr6 [121756779, 121756813]      * |      4.0000      breast      CEEHRC
    [3]     chr6 [121756813, 121756872]      * |      3.0000      breast      CEEHRC
    [4]     chr6 [121756872, 121756899]      * |      2.0000      breast      CEEHRC
    [5]     chr6 [121756899, 121756916]      * |      1.0000      breast      CEEHRC
    ...      ...                    ...    ... .         ...         ...         ...
  [468]     chr6 [121770753, 121770805]      * |      1.0000      breast      CEEHRC
  [469]     chr6 [121770805, 121770857]      * |      2.0000      breast      CEEHRC
  [470]     chr6 [121770857, 121770860]      * |      3.0000      breast      CEEHRC
  [471]     chr6 [121770860, 121770863]      * |      4.0000      breast      CEEHRC
  [472]     chr6 [121770863, 121770881]      * |      5.0000      breast      CEEHRC
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

 

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Entering edit mode
@helimelanie-15780
Last seen 4.6 years ago

Exactly what I needed! Thank you so much for your help! 

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