qtn_linkage: Select SNPs to be assigned as QTNs

In simplePHENOTYPES: Simulation of Pleiotropic, Linked and Epistatic Phenotypes

Description

Select SNPs to be assigned as QTNs

Usage

qtn_linkage(
  genotypes = NULL,
  seed = NULL,
  add_QTN_num = NULL,
  dom_QTN_num = NULL,
  ld_max = NULL,
  ld_min = NULL,
  ld_method = "composite",
  gdsfile = NULL,
  constraints = list(maf_above = NULL, maf_below = NULL),
  rep = NULL,
  rep_by = NULL,
  export_gt = NULL,
  same_add_dom_QTN = NULL,
  add = NULL,
  dom = NULL,
  type_of_ld = NULL,
  verbose = verbose
)

Arguments

genotypes	= NULL,
seed	= NULL,
add_QTN_num	= NULL,
dom_QTN_num	= NULL,
ld_max	= NULL,
ld_min	= NULL,
ld_method	Four methods can be used to calculate linkage disequilibrium values: "composite" for LD composite measure, "r" for R coefficient (by EM algorithm assuming HWE, it could be negative), "dprime" for D', and "corr" for correlation coefficient.
gdsfile	NULL
constraints	= list(maf_above = NULL, maf_below = NULL)
rep	= 1,
rep_by	= 'QTN',
export_gt	= FALSE
same_add_dom_QTN	= NULL,
add	= NULL,
dom	= NULL,
type_of_ld	= NULL
verbose	= verbose

Value

Genotype of selected SNPs

Author(s)

Samuel Fernandes Last update: Apr 20, 2020

—————————– QTN_linkage ————————————

simplePHENOTYPES documentation built on Jan. 20, 2021, 5:09 p.m.