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Update sumstats_qc.R #466

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10 changes: 9 additions & 1 deletion R/sumstats_qc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -26,10 +26,18 @@ rss_basic_qc <- function(sumstats, LD_data, skip_region = NULL, keep_indel = TRU
stop("Missing columns in sumstats: ", paste(missing_cols, collapse = ", "))
}

# Dynamically detect which effect columns exist to flip
# Must have at least one of beta or z
flip_candidates <- c("beta", "z")
col_to_flip <- intersect(flip_candidates, colnames(sumstats))
if (length(col_to_flip) == 0) {
stop("sumstats must contain at least one of: 'beta', 'z'")
}

ref_variants <- LD_data$LD_variants

allele_flip <- allele_qc(sumstats, ref_variants,
col_to_flip = c("beta", "z"),
col_to_flip = col_to_flip,
match_min_prop = 0, remove_dups = TRUE, remove_indels = !keep_indel,
remove_strand_ambiguous = TRUE
)
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