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mv_extract_exposures_local possibility to include a dataframe already clumped #569

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AngeTKL opened this issue Oct 2, 2024 · 0 comments

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@AngeTKL
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AngeTKL commented Oct 2, 2024

i will like to raise an issue here. could it be possible to adapt the code so that if you have a short list of snps already clumped (e.g stroke), the function will harmonize without clumping stroke.csv but only clump obesity.csv. the user can choose which ever dataframe he want to be clumped prior.

exposure_dat <- mv_extract_exposures_local(
filenames_exposure = c('stroke.csv', 'Obesity.csv'),
sep = ",",
phenotype_col = "Phenotype",
snp_col = "SNP",
beta_col = "beta",
se_col = "se",
eaf_col = "eaf",
effect_allele_col = "effect_allele",
other_allele_col = "other_allele",
pval_col = "pval",
units_col = "units",
ncase_col = "ncase",
ncontrol_col = "ncontrol",
samplesize_col = "samplesize",
gene_col = "gene",
id_col = "id",
min_pval = 1e-200,
log_pval = FALSE,
pval_threshold = 5e-08,
plink_bin = NULL,
bfile = NULL,
clump_r2 = 0.001,
clump_kb = 10000,
pop = "EUR",
harmonise_strictness = 3 )

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