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Compute per-annotation standard deviation, MAF-restricted

Source: R/sldsc_wrapper.R
compute_sldsc_annot_sd.Rd

Computes the standard deviation of each annotation column in the target annotation files, restricted to SNPs above a MAF cutoff via PLINK `.frq` files. Required for internal consistency with polyfun's regression, which operates on MAF > cutoff SNPs by default.

Usage

compute_sldsc_annot_sd(
  target_anno_dir,
  frqfile_dir = NULL,
  plink_name = "ADSP_chr",
  maf_cutoff = 0.05,
  annot_cols = NULL
)

Arguments

target_anno_dir

Character. Directory containing target annotation files (one per chromosome) in polyfun's `.annot.gz` format.

frqfile_dir

Character or NULL. Directory containing PLINK `.frq` files for the reference panel. Required when `maf_cutoff > 0`; the function errors if missing.

Character. Filename prefix of the `.frq` files (e.g. `"ADSP_chr"`). Files are expected at `plink_namechr.frq`.

maf_cutoff

Numeric, default `0.05`.

annot_cols

Character or integer vector, default NULL. Annotation columns to compute sd for. If NULL, all annotation columns are used.

Value

Named numeric vector of \(sd_C\) values, one per annotation.