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December 5, 2025 07:58
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BMI-alcohol-ancestry interaction
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| library(dplyr) | |
| library(data.table) | |
| library(seqminer) | |
| library(stringr) | |
| dat <- fread("/mnt/project/analysis/bmi-alcohol-ancestry/phen_extract.csv") | |
| str(dat) | |
| anc <- fread("/mnt/project/data/ancestry/ukb_InferredAncestry.txt") | |
| str(anc) | |
| sampleinfo_colnames <- stringr::str_replace_all( | |
| tolower(c( | |
| "x1", | |
| "x2", | |
| "genotyping.array", | |
| "Batch", | |
| "Plate.Name", | |
| "Well", | |
| "Cluster.CR", | |
| "dQC", | |
| "Internal.Pico..ng.uL.", | |
| "Submitted.Gender", | |
| "Inferred.Gender", | |
| "X.intensity", | |
| "Y.intensity", | |
| "Submitted.Plate.Name", | |
| "Submitted.Well", | |
| "sample.qc.missing.rate", | |
| "heterozygosity", | |
| "heterozygosity.pc.corrected", | |
| "het.missing.outliers", | |
| "putative.sex.chromosome.aneuploidy", | |
| "in.kinship.table", | |
| "excluded.from.kinship.inference", | |
| "excess.relatives", | |
| "in.white.British.ancestry.subset", | |
| "used.in.pca.calculation", | |
| paste("pc", 1:40, sep = ""), | |
| "in.Phasing.Input.chr1_22", | |
| "in.Phasing.Input.chrX", | |
| "in.Phasing.Input.chrXY" | |
| )), | |
| "[[:punct:]]", "_" | |
| ) | |
| sampleinfo <- fread("/mnt/project/Bulk/Genotype Results/Genotype calls/ukb_sqc_v2.txt") | |
| colnames(sampleinfo) <- sampleinfo_colnames | |
| str(sampleinfo) | |
| bg.ref.file <- "/mnt/project/Bulk/Imputation/Imputation from genotype (TOPmed)/ukb21007_c4_b0_v1.bgen" | |
| file.exists(bg.ref.file) | |
| bg.range <- "chr4:99318162-99318162" | |
| geno.mat <- seqminer::readBGENToMatrixByRange(bg.ref.file, bg.range) | |
| samplefile <- fread("/mnt/project/Bulk/Imputation/Imputation from genotype (TOPmed)/ukb21007_c4_b0_v1.sample", skip=2, header=FALSE) | |
| str(samplefile) | |
| str(geno.mat) | |
| dim(geno.mat[[1]]) | |
| str(geno.mat[[1]]) | |
| # Combine everything | |
| # genotype | |
| # phenotypes | |
| # ancestry | |
| # PCs | |
| table(samplefile$V1 %in% sampleinfo$x2) | |
| table(samplefile$V1 %in% dat$eid) | |
| table(samplefile$V1 %in% anc$IID) | |
| dim(sampleinfo) | |
| dim(samplefile) | |
| str(dat) | |
| d <- inner_join(dat, anc %>% select(IID, PC1, PC2, ANC=Anc_1st), by=c("eid"="IID")) | |
| g <- tibble(eid=samplefile$V2, geno=drop(t(geno.mat[[1]]))) | |
| d <- inner_join(d, g) | |
| str(d) | |
| summary(lm(p21001_i0 ~ geno + PC1 + PC2, d)) | |
| summary(lm(p21001_i0 ~ geno + PC1 + PC2, d)) | |
| summary(lm(geno ~ p1558_i0 + PC1 + PC2, d)) | |
| d <- mutate(d, | |
| alcohol = case_when( | |
| p1558_i0 == "Never" ~ 0, | |
| p1558_i0 == "Special occasions only" ~ 1, | |
| p1558_i0 == "One to three times a month" ~ 2, | |
| p1558_i0 == "Once or twice a week" ~ 3, | |
| p1558_i0 == "Three or four times a week" ~ 4, | |
| p1558_i0 == "Daily or almost daily" ~ 5, | |
| TRUE ~ NA | |
| )) | |
| table(d$alcohol) | |
| table(d$alcohol, d$ANC) | |
| summary(lm(p21001_i0 ~ geno * ANC, d)) | |
| summary(lm(p21001_i0 ~ geno * alcohol, d %>% filter(ANC == "EUR"))) | |
| summary(lm(p21001_i0 ~ geno * alcohol + geno * ANC, d)) | |
| summary(lm(p21001_i0 ~ geno * alcohol, d %>% filter(ANC == "SAS"))) | |
| summary(lm(alcohol ~ geno, d %>% filter(ANC == "EUR"))) | |
| summary(lm(alcohol ~ geno, d %>% filter(ANC == "EUR"))) | |
| summary(lm(p21001_i0 ~ geno, d %>% filter(ANC == "EUR"))) | |
| summary(lm(p21001_i0 ~ geno + alcohol, d %>% filter(ANC == "EUR"))) |
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