viewpoly (version 0.4.1)

prepare_qtl_custom_files: Converts QTL information in custom files to viewqtl object

Description

Converts QTL information in custom files to viewqtl object

Usage

prepare_qtl_custom_files(
  selected_mks,
  qtl_info,
  blups,
  beta.hat,
  profile,
  effects,
  probs
)

Value

object of class viewqtl

Arguments

selected_mks

data.frame with: LG - linkage group ID; mk - marker ID; pos - position in linkage map (cM)

qtl_info

data.frame with: LG - linkage group ID; Pos - position in linkage map (cM); Pheno - phenotype ID; Pos_lower - lower position of confidence interval; Pos_upper - upper position of the confidence interval; Pval - QTL p-value; h2 - herdability

blups

data.frame with: haplo - haplotype ID; pheno - phenotype ID; qtl - QTL ID; u.hat - QTL estimated BLUPs

beta.hat

data.frame with: pheno - phenotype ID; beta.hat - estimated beta

profile

data.frame with: pheno - phenotype ID; LOP - significance value for the QTL, in this case LOP (can be LOD or DIC depending of the software used)

effects

data.frame with: pheno - phenotype ID; qtl.id - QTL ID; haplo - haplotype ID; effect - haplotype effect value

probs

data.frame with first column (named `ind`) as individuals ID and next columns named with markers ID and containing the genotype probability at each marker