Man pages for viewpoly
A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

breeding_valuesEstimate breeding values - Adapted function from QTLpoly
calc_homologprobCalculates homologues probabilities - Adapted from MAPpoly
check_viewmapViewmap object sanity check
check_viewpolyViewpoly object sanity check
check_viewqtlviewqtl object sanity check
coord_radarChange ggplot coordinates to plot radar - From package see
data_effectsGet effects information
dist_prob_to_classReturns the class with the highest probability in a genotype...
draw_map_shinyDraws linkage map, parents haplotypes and marker doses...
filter_non_conforming_classesFilter non-conforming classes in F1, non double reduced...
get_LODExtract the LOD Scores in a "" object Function...
gg_color_hueColor pallet ggplot-like - Adapted from MAPpoly
imf_hMap functions - from MAPpoly
import_data_from_polymapRImport data from polymapR
import_phased_maplist_from_polymapRImport phased map list from polymapR
is.prob.dataIs it a probability dataset? Function from MAPpoly.
map_summaryGets summary information from map. Adapted from MAPpoly
mf_hHaldane map function. From MAPpoly
mrk_chisq_testChi-square test. Function from MAPpoly.
only_plot_profileOnly the plot part of plot_profile function
ph_list_to_matrixLinkage phase format conversion: list to matrix. Function...
ph_matrix_to_listLinkage phase format conversion: matrix to list. Function...
plot_cm_mbScatter plot relating linkage map and genomic positions
plot_effectsPlot effects data
plot_map_listPlot a genetic map - Adapted from MAPpoly
plot.mappoly.homoprobPlots mappoly.homoprob from MAPpoly
plot_one_mapPlot a single linkage group with no phase - from MAPpoly
plot_profileLogarithm of _P_-value (LOP) profile plots. Modified version...
prepare_diaQTLConverts diaQTL output to viewqtl object
prepare_examplesUpload example files
prepare_mapprepare maps for plot - from MAPpoly
prepare_map_custom_filesConverts map information in custom format files to viewmap...
prepare_MAPpolyConverts list of object into viewmap object
prepare_polymapRConverts polymapR ouputs to viewmap object
prepare_polyqtlRConverts polyqtlR outputs to viewqtl object
prepare_qtl_custom_filesConverts QTL information in custom files to viewqtl object
prepare_QTLpolyConverts QTLpoly outputs to viewqtl object
run_appRun the Shiny Application
segreg_polyPolysomic segregation frequency - Function from MAPpoly
select_haploPlot selected haplotypes
summary_mapsSummary maps - adapted from MAPpoly
viewpoly documentation built on Nov. 2, 2022, 1:05 a.m.