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update function names #390

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Merged
gaow merged 1 commit into from
May 20, 2025
Merged

update function names #390

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14 changes: 13 additions & 1 deletion R/allele_qc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -63,8 +63,20 @@ allele_qc <- function(target_data, ref_variants, col_to_flip = NULL,
}

# transform all inputs to dataframe
if (is.data.frame(target_data)) {
if (ncol(target_data) > 4 && all(c("chrom", "pos", "A2", "A1") %in% names(target_data))) {
# Extract variant columns and standardize
variant_cols <- c("chrom", "pos", "A2", "A1")
variant_df <- target_data %>% select(all_of(variant_cols))
other_cols <- target_data %>% select(-all_of(variant_cols))
target_data <- cbind(variant_id_to_df(variant_df), other_cols)
} else {
target_data <- variant_id_to_df(target_data)
}
} else {
target_data <- variant_id_to_df(target_data)
}
ref_variants <- variant_id_to_df(ref_variants)
target_data <- variant_id_to_df(target_data)
columns_to_remove <- c("chromosome", "position", "ref", "alt", "variant_id")

# Check if any of the specified columns are present
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