robinweide / GENOVA

GENome Organisation Visual Analytics
GNU General Public License v3.0
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Problem in loading data #283

Closed canfeng-HUA closed 2 years ago

canfeng-HUA commented 2 years ago

Describe the bug I meet some problems when I load the data. Could you please help me fix it?

To Reproduce Steps to reproduce the behavior:

WT_KB_matrix <- load_contacts(
+   signal_path = "./data/HI-C-WT-KB_27000_iced.matrix",
+   indices_path = "./data/HI-C-hrpL-KB_27000_abs.bed",
+   sample_name = "WT-KB",
+   resolution = 27000,
+   colour = "black")

Reading data... Error in set(x, j = name, value = value) : Supplied 18005 items to be assigned to 18216 items of column 'C1'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code.

Expected behavior No error. My data can be loaded in the package

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teunbrand commented 2 years ago

Hi there,

Thank you for the report. Would you mind posting the head and tail (with n = 5 or so) of the ./data/HI-C-WT-KB_27000_iced.matrix and ./data/HI-C-hrpL-KB_27000_abs.bed files? The bug sounds akin to #276.

Best, Teun

canfeng-HUA commented 2 years ago

Thanks a lot for your suggestion! I solve this problem. I add the title to the <.bed> file and solve this problem, following the suggestion from #276

But I meet a new problem image

here is the head and tail of my bed files image