Get Top Loci (posterior view)

Extract the per-variant posterior fine-mapping payload as either a data.frame (default) or a GRanges. Returns identity columns (variant_id, chrom, pos, A1, A2), context (N, MAF), the posterior effect columns (beta = posterior_mean, se = posterior_sd), pip, and credible-set membership columns (cs_95, etc.). Rows are filtered by PIP by default — set signalCutoff = 0 to return every variant.

Usage

getTopLoci(x, type = c("data.frame", "GRanges"), signalCutoff = 0.025, ...)

# S4 method for class 'FineMappingResultBase'
getTopLoci(
  x,
  type = c("data.frame", "GRanges"),
  signalCutoff = 0.025,
  study = NULL,
  context = NULL,
  trait = NULL,
  method = NULL,
  region = NULL,
  minPurity = NULL,
  ...
)

# S4 method for class 'FineMappingEntry'
getTopLoci(
  x,
  type = c("data.frame", "GRanges"),
  signalCutoff = 0.025,
  minPurity = NULL,
  ...
)

Arguments

x

A FineMappingEntry or FineMappingResult.

type

One of "data.frame" (default) or "GRanges".

signalCutoff

Numeric (length 1). Drop rows where pip <= signalCutoff. Default 0.025. Use signalCutoff = 0 to keep every variant.

...

Class-specific selection arguments.

Value

A data.frame or a GRanges.