inputs: Upload example files

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

Description

Upload example files

Converts map information in custom format files to viewmap object

Converts list of mappoly.map object into viewmap object

Converts polymapR ouputs to viewmap object

Converts QTLpoly outputs to viewqtl object

Converts diaQTL output to viewqtl object

Converts polyqtlR outputs to viewqtl object

Converts QTL information in custom files to viewqtl object

Usage

prepare_examples(example)

prepare_map_custom_files(dosages, phases, genetic_map)

prepare_MAPpoly(mappoly_list)

prepare_polymapR(polymapR.dataset, polymapR.map, input.type, ploidy)

prepare_QTLpoly(data, remim.mod, est.effects, fitted.mod)

prepare_diaQTL(scan1_list, scan1_summaries_list, fitQTL_list, BayesCI_list)

prepare_polyqtlR(polyqtlR_QTLscan_list, polyqtlR_qtl_info, polyqtlR_effects)

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

Arguments

dosages	TSV or TSV.GZ file with both parents dosage information. It should contain four columns: 1) character vector with chromosomes ID; 2) Character vector with markers ID; 3) Character vector with parent ID; 4) numerical vector with dosage.
phases	TSV or TSV.GZ file with phases information. It should contain: 1) Character vector with chromosome ID; 2) Character vector with marker ID; 3 to (ploidy number)*2 columns with each parents haplotypes.
genetic_map	TSV or TSV.GZ file with the genetic map information
mappoly_list	list with objects of class mappoly.map
data	object of class "qtlpoly.data"
remim.mod	object of class "qtlpoly.model" "qtlpoly.remim".
est.effects	object of class "qtlpoly.effects"
fitted.mod	object of class "qtlpoly.fitted"

Author(s)

Cristiane Taniguti, [e-mail]

viewpoly documentation built on Jan. 3, 2022, 5:10 p.m.