GeneArchEst: Estimate Genomic Architecture for Quantitative Traits

calc_distribution_stats

R Documentation

Calculates statistics for GWAS or prediction effect/p-value distributions.

Description

Given genotypic data, calculates descriptive statistics of GWAS/gp results or compares those results to that from the real data.

Usage

calc_distribution_stats(
  x = NULL,
  meta,
  phenos,
  center = T,
  scheme = "gwas",
  chr = "chr",
  peak_delta = 0.5,
  peak_pcut = 5e-04,
  window_sigma = 50,
  burnin = NULL,
  thin = NULL,
  chain_length = NULL,
  maf = 0.05,
  phased = FALSE,
  pass_windows = F,
  pass_G = NULL,
  GMMAT_infile = NULL,
  find_similar_effects = FALSE,
  real_effects = NULL,
  save_effects = FALSE
)

Arguments

`meta`	data.frame. A data.frame containing SNP metadata. Must have a column containing chromosome info (named to match the "chr" argument) and another named "position" containing position information in base pairs.
`phenos`	numeric. A vector of phenotypes.
`scheme`	"gwas" or "gp", default "gwas". Method to use.
`chr`	character, default "chr". Name of the metadata column containing chromosome information.
`find_similar_effects`	logical, default F. If F, calculates descriptive stats for the effects. If T, compares distribution to the "real_effects" data.
`real_effects`	numeric or NULL, default NULL. If provided and find_similar_effects is TRUE, this effect distribution is compared to that for the provided geno/phenotypes. This can be calculated for the real data using `pred_GWAS_FBM`.
`save_effects`	character or FALSE, default FALSE. If true, simulated effects will be appended to filepath provided here.
`Object`	coercable to matrix or NULL, default NULL. If provided, a matrix coercable object containing genotype calls. If NULL, a GMMAT infile must instead be provided.