prepare_qtl_custom_files: Converts QTL information in custom files to viewqtl object

In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

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
)

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

Value

object of class viewqtl

viewpoly documentation built on May 29, 2024, 1:26 a.m.