Question

visualize Hi-C .cool file in R

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ta_awwad ▴ 10

@ta_awwad-11382

Last seen 5 months ago

Frankfurt am Main

Hello everyone,

I am really new in visualising Hi-C data. Now I have normalized .cool files and I would like to visiualize it in R using HiTC package .. my .cool files are in the following format:

chrom1    start1    end1    chrom2    start2    end2    count    balanced

chr18    10500000    10600000    chr18    10500000    10600000    1163    0.0482848

chr18    10500000    10600000    chr18    10600000    10700000    574    0.0397891

chr18    10500000    10600000    chr18    10700000    10800000    588    0.0312273

chr18    10500000    10600000    chr18    10800000    10900000    602    0.0255296

chr18    10500000    10600000    chr18    10900000    11000000    446    0.0186205

chr18    10500000    10600000    chr18    11000000    11100000    413    0.0167251

chr18    10500000    10600000    chr18    11100000    11200000    182    0.00995996

chr18    10500000    10600000    chr18    11200000    11300000    192    0.0109431

chr18    10500000    10600000    chr18    11300000    11400000    147    0.00932337

can anyone help?

many many thanks

TA

Hi-C HiTC • 1.8k views

ADD COMMENT • link 6.4 years ago ta_awwad ▴ 10

1

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Hi,

So far, there is no ready-to-use function to do import cool file into R (at least with HiTC).

But it should be quite straighforward to write. You can have a look at the importC function as a template.

Otherwise, I can do it for the next release.

Best

Nicolas

ADD REPLY • link 6.4 years ago Nicolas Servant ▴ 260

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Thanks much Nicolas for your quick reply .. it would be great if you implement these functions to be suitable to import several Hi-C output formats

Best

TA

ADD REPLY • link 6.4 years ago ta_awwad ▴ 10

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I managed to get the interaction matrix .. in my case 878 X 878 .. also I prepared the Granges of the interaction bins (878 Grange) .. now when I am trying to construct HTCexp object gives me the following error message:

Error in dimnamesGets(x, value) : 
  invalid dimnames given for “dsyMatrix” object

what could be possibly wrong?

thanks much

TA

ADD REPLY • link 6.4 years ago ta_awwad ▴ 10

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In the HTCexp object, dimnames of the matrix (ie. colnames/rownames) should match the names of the GRanges object. I think it explains the error.

N

ADD REPLY • link 6.4 years ago Nicolas Servant ▴ 260

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Thanks much it was really stupid question ... now everything works fine ..thanks once more

TA

ADD REPLY • link 6.4 years ago ta_awwad ▴ 10