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Reference-panel SNP count (the M_ref used to standardise tau*)

Source: R/sldscWrapper.R
computeSldscMRef.Rd

`M_ref` is the number of SNPs in the REFERENCE PANEL over which heritability is partitioned in the sLDSC model (`h2(C) = sum_j in M_ref a_C(j) sum_C' tau_C' a_C'(j)`). It is panel-defined and is **not** the regression SNP set (HapMap3 ~1M) nor any HM3-subsetted target output:

  • `mafCutoff > 0` (Gazal/Finucane convention): count MAF > cutoff SNPs across all `.frq` files (the same set polyfun's `.l2.M_5_50` sums).

  • `mafCutoff == 0` (all-M variant): count ALL SNPs across all `.frq` files (the same set polyfun's `.l2.M` sums).

When no frq data is present, `mafCutoff == 0` falls back to the number of annotation rows; `mafCutoff > 0` errors (a MAF-restricted count needs frq).

Usage

computeSldscMRef(sldscData, mafCutoff = 0.05)

Arguments

sldscData

An SldscData object (its frq slot is the reference-panel SNP set).

mafCutoff

Numeric, default `0.05`.

Value

Scalar integer.