PCA projection with --score plink2.sscore output: what are the ALLELE_CT & NAMED_ALLELE_DOSAGE

PCA projection with --score plink2.sscore output: what are the ALLELE_CT & NAMED_ALLELE_DOSAGE_SUM showing?

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22 months ago

ucbtep ▴ 20

Hi - I'm fairly new to populations genetics and plink2, and have a couple of questions about the output file generated when completing PCA projection with --score using plink2.

Following the plink2 instructions (see here, https://www.cog-genomics.org/plink/2.0/score#pca_project) I have created population covariates in my sample using --score. This generates a plink2.sscore file, which contains columns for FID and IID, the PCs (i.e., PC1-10_AVG) and also "ALLELE_CT" & "NAMED_ALLELE_DOSAGE_SUM".

Please could someone explain what the columns "ALLELE_CT" & "NAMED_ALLELE_DOSAGE_SUM" are showing?

Thanks in advance!

pca-projection allele-dosage score plink2 • 1.4k views

ADD COMMENT • link updated 22 months ago by chrchang523 11k • written 22 months ago by ucbtep ▴ 20

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Did you look at https://www.cog-genomics.org/plink/2.0/formats#sscore ?

ADD REPLY • link 22 months ago by chrchang523 11k

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Thank you chrchang523 . After reading the information for the "NAMED_ALLELE_DOSAGE_SUM" variable (i.e., that it is the sum of named allele dosages) I'm not sure what it is showing, partly because there is one "NAMED_ALLELE_DOSAGE_SUM" variable but 10 PCs in the output. Could someone explain?