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bcm-uga / pcadapt

Performing highly efficient genome scans for local adaptation with R package pcadapt v4
https://bcm-uga.github.io/pcadapt
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How to obtain the specific sites of outliers #89

Open xiangping2023 opened 4 months ago

xiangping2023 commented 4 months ago

I'm very sorry to bother you. I have been reading your three articles on the use of pcadapt for detecting signals of natural selection, and I am very interested in the topic. I have also tried the preliminary analysis using the code you provided on GitHub, and everything has been going smoothly. However, after performing the analysis with a bed input file, I have encountered a slight issue. While I am able to determine the number of outliers, I am unable to identify the specific SNPs at these outlier positions. I am eager to find a solution that would allow me to identify not only the number of outliers but also the exact SNPs at these positions. I would greatly appreciate any advice or suggestions you could provide to help me with this matter. We hope you can give us some suggestions. Thank you very much for your time and assistance.

privefl commented 4 months ago

You need to read the corresponding .bim file to find information on the variants in the data.

Lin012345 commented 4 months ago

You need to read the corresponding .bim file to find information on the variants in the data.

Thank you for your response, but I am still a bit confused. Could you provide more detailed information on reading the corresponding .bim and identifying specific SNPs?Thank you for your patient answers

privefl commented 4 months ago

This is just a text file with information on the variants. It should be in the same order as the results from pcadapt.

Lin012345 commented 3 months ago

This is just a text file with information on the variants. It should be in the same order as the results from pcadapt.

Thank you very much for your patient explanation. I will attempt it in the subsequent analysis, and I am grateful for your amazing work.