CarlKCarlK
commented
2 years ago Yes,
FaST-LMM is just as happy to run on a "SnpData" as on a "Bed".
Here is a simple example of creating a tiny SnpData object:
from pysnptools.snpreader import SnpData
snpdata = SnpData(iid=[['fam0','iid0'],['fam0','iid1']], sid=['snp334','snp349','snp921'], val=[[0.,2.,0.],[0.,1.,2.]]) print((snpdata.val[0,1], snpdata.iid_count, snpdata.sid_count)) (2.0, 2, 3)
You'll notice that you pass "SnpData(...)" a list of family/individual id names, a list of SNP names, and a 2D array of values. In this case, the SnpData was created without chromosome information, so it defaults to chromosome "0". You can change this with an additional line:
snpdata.pos[:,0] = [1,1,2] # assign the first and 2nd SNP to chrom 1 and 3rd to chrom 2
There is more info at: https://fastlmm.github.io/PySnpTools/#snpreader-snpdata
Put another way - If you can write Python code that gets this information from VCF files (or any other format):
- Family and SNP ids
- SNP ids
- Chromosome number
- A 2-D array of values 0,1,2 and missing (representing the allele count) Then you can create a SnpData and then you can call FaST-LMM.
If you can extract this info from your VCF files (or any other sources), I'm happy to help you get FaST-LMM running on this info.
- Carl
From: snowformatics @.> Sent: Monday, August 01, 2022 12:37 AM To: fastlmm/FaST-LMM @.> Cc: Subscribed @.***> Subject: [fastlmm/FaST-LMM] Run without PLINK format (Issue #30) Importance: High
Hi,
I have a short question, is it possible to run FaST-LMM without PLINK Bed format? If I understand correctly, single_snp function run with any SnpReader format which could be also SnpData. Is this correct? What about the FAM and BIM file, are there required? I want to add an alternative option without using PLINK and work with the VCF directly or often users have only the SNP matrix available.
Thanks Stefanie
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snowformatics
Hi,
I have a short question, is it possible to run FaST-LMM without PLINK Bed format? If I understand correctly, single_snp function run with any SnpReader format which could be also SnpData. Is this correct? What about the FAM and BIM file, are there required? I want to add an alternative option without using PLINK and work with the VCF directly or often users have only the SNP matrix available.
Thanks Stefanie