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zhengxwen / HIBAG

R package – HLA Genotype Imputation with Attribute Bagging (development version only)
https://hibag.s3.amazonaws.com/index.html
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association test #19

Closed SunYidan2021 closed 1 year ago

SunYidan2021 commented 1 year ago

Hi Xiuwen, I would like to ask how to understand the result of the association test. Is it necessary to calculate the Bonferroni-corrected p-values? I also have some questions on convert alleles to Plink format. If I understand correctly, genotyped information is needed in this process. However, I would like to ask if it is possible to directly convert hlaAllele to Plink format. Thank you in advance!

zhengxwen commented 1 year ago

Whether you need Bonferroni correction or not depends on your scientific question. Try hlaAlleleToVCF() to convert hlaAllele to PLINK.

hlaAlleleToVCF(hla, outfn, DS=TRUE, verbose=TRUE)
SunYidan2021 commented 1 year ago

Hi Xiuwen, I try to use this function, however, I got an error. Error in hlaAlleleToVCF() : could not find function "hlaAlleleToVCF"

zhengxwen commented 1 year ago

Update the version of the HIBAG package.

CHANGES IN VERSION 1.28.0

o new function `hlaAlleleToVCF()` for converting the imputed HLA classical alleles to a VCF file