Hello everyone,
First of all, I want to say thank you for providing a large amount of educational materials.
Using Python, I have obtained a CSV file with phenotypic data. I have also downloaded genetic data from Bulk/Exome sequences/Population level exome OQFE variants, PLINK format - final release/ for the required chromosome and filtered the genetic data for the required positions in the chromosome, and now it is in MatrixTable.
My question is, how can I enrich the phenotypic data, which is represented as a Pandas DataFrame, with the genetic data that is in MatrixTable? I would like to obtain a Pandas DataFrame that is augmented with the genetic data.
Next, I want to analyze this DataFrame. Since this is an urgent question, I would appreciate a detailed and prompt response.
Thank you for your response and for sharing the helpful tips in the thread. Unfortunately, I have not been able to successfully combine the pandas DataFrame with the phenotypic data and the Hail table with the filtered genetic data that I need. I appreciate your patience and understanding as I continue to work on this.
Comments
2 comments
I shared some tips in this thread: https://community.dnanexus.com/s/question/0D582000000Kk8OCAS/selecting-snps-of-interest-and-linking-these-selected-snps-to-rest-of-data
Hello @Ondrej Klempir? ,
Thank you for your response and for sharing the helpful tips in the thread. Unfortunately, I have not been able to successfully combine the pandas DataFrame with the phenotypic data and the Hail table with the filtered genetic data that I need. I appreciate your patience and understanding as I continue to work on this.
Thank you again.
Best,
Alex
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