Bioinformatics Asked on April 28, 2021
When we use local data using TwoSampleMR, how can we assign LD proxies where the outcome data is not available?
https://mrcieu.github.io/TwoSampleMR/articles/outcome.html
outcome_dat <- read_outcome_data(
snps = bmi_exp_dat$SNP,
filename = "gwas_summary.csv",
sep = ",",
snp_col = "rsid",
beta_col = "effect",
se_col = "SE",
effect_allele_col = "a1",
other_allele_col = "a2",
eaf_col = "a1_freq",
pval_col = "p-value",
units_col = "Units",
gene_col = "Gene",
samplesize_col = "n"
)
When we use "extract_outcome_data", we can automatically assign LD proxies, but this cannot be applied to local data.
chd_out_dat <- extract_outcome_data(
snps = bmi_exp_dat$SNP,
outcomes = 'ieu-a-7'
)
#> Extracting data for 79 SNP(s) from 1 GWAS(s)
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