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Get Standardized Sumstat Data Frame for One Tuple

Source: R/AllGenerics.R, R/qtlSumStats.R, R/gwasSumStats.R
getSumstatDf.Rd

Return a per-tuple summary-statistics data.frame in the standardized layout variant_id, chrom, pos, A1, A2, z, beta, se, N, maf (optional columns omitted when absent on the entry). Combines tuple-keyed row selection (getSumStats) with mcols unpacking; replaces the pre-S4 idiom of pulling S4Vectors::mcols(entry)$<col> directly inside pipelines.

Usage

getSumstatDf(x, ...)

# S4 method for class 'QtlSumStats'
getSumstatDf(
  x,
  study = NULL,
  context = NULL,
  trait = NULL,
  require = character(0),
  derive = c("none", "zFromBetaSe"),
  keepChrPrefix = TRUE
)

# S4 method for class 'GwasSumStats'
getSumstatDf(
  x,
  study = NULL,
  require = character(0),
  derive = c("none", "zFromBetaSe"),
  keepChrPrefix = TRUE
)

Arguments

x

A GwasSumStats or QtlSumStats object.

...

Class-specific selectors (study for GwasSumStats; study, context, trait for QtlSumStats) plus pass-throughs require, derive, keepChrPrefix forwarded to the underlying unpacker.

Value

A data.frame.