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wegene-llc / radmixture

an R package for ancestry analysis
https://CRAN.R-project.org/package=radmixture
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Working with non-default datasets #7

Open LorenzoLF opened 3 years ago

LorenzoLF commented 3 years ago

Hello,

I have been working with the package and it works like a charm with the default datasets included in the package (K4, K9, world 9 and so on). However, I have found that the results do not make sense when I use other datasets.

For example, I have used the MAF report for the 24 populations of the 1000Genomes project that one can find for the most commonly used SNP arrays (ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/productfiles/global-screening-array/v2-0/infinium-global-screening-array-24-v2-0-a1-population-reports-maf-copy-numbers.zip). Although the software does run with this frequency file (and the corresponding alleles file), the results are nonsense.

I would appreciate if somebody could help me in this regard or confirm whether this package has been used with non-default datasets successfully. My objective is to get it to run with more than 13 population groups (which is the maximum number in the default packages).

Thank you very much.

tomatoiscoding commented 3 years ago

How many individuals in your dataset? I wouldn't recommend you to use this R package if you're working on a large-scale dataset. You can use ADMIXTURE directly which is faster than R.

LorenzoLF commented 3 years ago

Thank you very much for your reply. I will indeed try that!