I realize that there is a txt-file for each chromosome, with patients as columns and genes as rows. I would need to find the CNV levels for one particular gene for a cohort of patients. Where can I find the metadata for these files or what would be the appropriate call in python?
I looked into it, but I don't think this is possible the way it is. The data is just a text with no header, column or row name. I can't really tell which variant or individual each value came from.
I recommend you to contact UKB data access team to provide more information. There might be a separate file that has row or column name. If we have that, when we can show how to use Python to extract location that you need.
Hello @Elena Jolkver?, have you received any answer back from UKB? I would be really interested in knowing how to read this data in Python.
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Yes, I reached out to the data access team and this is their reply:
"The rows correspond to markers (ordered as the calls BIM file) and the columns correspond to samples (ordered as the calls in the FAM file) Missing values are represented by -1. These BIM and FAM files are from the genotype calls (field 22418) , and can be found in the RAP folder: Bulk/Genotype Results/Genotype calls/
These BIM and FAM files (one per chromosome) should allow you to determine genes and participants within the log2ratio file."
So I retrieved the information from those files and assigned column/rownames to the cnv file. I was actually expecting a cnv call on a gene level, but the files provide it on SNP level.
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I looked into it, but I don't think this is possible the way it is. The data is just a text with no header, column or row name. I can't really tell which variant or individual each value came from.
I recommend you to contact UKB data access team to provide more information. There might be a separate file that has row or column name. If we have that, when we can show how to use Python to extract location that you need.
Hello @Elena Jolkver?, have you received any answer back from UKB? I would be really interested in knowing how to read this data in Python.
Yes, I reached out to the data access team and this is their reply:
"The rows correspond to markers (ordered as the calls BIM file) and the columns correspond to samples (ordered as the calls in the FAM file) Missing values are represented by -1. These BIM and FAM files are from the genotype calls (field 22418) , and can be found in the RAP folder: Bulk/Genotype Results/Genotype calls/
These BIM and FAM files (one per chromosome) should allow you to determine genes and participants within the log2ratio file."
So I retrieved the information from those files and assigned column/rownames to the cnv file. I was actually expecting a cnv call on a gene level, but the files provide it on SNP level.
Perfect! Thank you.
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