Help for package viewpoly

Title:

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

Version:

0.4.1

Maintainer:

Cristiane Taniguti <chtaniguti@tamu.edu>

Description:

Provides a graphical user interface to integrate, visualize and explore results from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid species. The app is meant for interactive use and allows users to optionally upload different sources of information, including gene annotation and alignment files, enabling the exploitation and search for candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.

License:

GPL (≥ 3)

Depends:

R (≥ 4.0)

Imports:

shiny (≥ 1.6.0), shinyjs, shinythemes, shinyWidgets, shinydashboard, config (≥ 0.3.1), golem (≥ 0.3.1), JBrowseR, dplyr, tidyr, DT, ggplot2, ggpubr, plotly, vroom, abind, reshape2, markdown, stats, hidecan, purrr

URL:

https://github.com/mmollina/viewpoly

BugReports:

https://github.com/mmollina/viewpoly/issues

Encoding:

UTF-8

RoxygenNote:

7.2.3

Suggests:

testthat (≥ 3.0.0), shinytest, rlang, pkgload, vdiffr

Config/testthat/edition:

Language:

en-US

NeedsCompilation:

Packaged:

2024-03-28 22:16:27 UTC; chtan

Author:

Cristiane Taniguti [aut, cre], Gabriel de Siqueira Gesteira [aut], Jeekin Lau [aut], Olivia Angelin-Bonnet [aut], Susan Thomson [ctb], Guilherme da Silva Pereira [ctb], David Byrne [ctb], Zhao-Bang Zeng [ctb], Oscar Riera-Lizarazu [ctb], Marcelo Mollinari [aut]

Repository:

CRAN

Date/Publication:

2024-03-28 22:30:02 UTC

Estimate breeding values - Adapted function from QTLpoly

Description

Estimate breeding values - Adapted function from QTLpoly

Usage

breeding_values(qtl_info, probs, selected_mks, blups, beta.hat, pos)

Arguments

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

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

selected_mks

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

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

pos

selected QTL position (cM)

Value

data.frame containing breeding values

Calculates homologues probabilities - Adapted from MAPpoly

Description

Calculates homologues probabilities - Adapted from MAPpoly

Usage

calc_homologprob(probs, selected_mks, selected_lgs)

Arguments

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

selected_mks

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

selected_lgs

vector containing selected LGs ID

Value

object of class mappoly.homoprob

Viewmap object sanity check

Description

Viewmap object sanity check

Usage

check_viewmap(viewmap_obj)

Arguments

viewmap_obj

an object of class viewmap

Value

if consistent, returns 0. If not consistent, returns a vector with a number of tests, where TRUE indicates a failed test.

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu

Viewpoly object sanity check

Description

Viewpoly object sanity check

Usage

check_viewpoly(viewpoly_obj)

Arguments

viewpoly_obj

an object of class viewpoly

Value

if consistent, returns 0. If not consistent, returns a vector with a number of tests, where TRUE indicates a failed test.

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu

viewqtl object sanity check

Description

viewqtl object sanity check

Usage

check_viewqtl(viewqtl_obj)

Arguments

viewqtl_obj

an object of class viewqtl

Value

if consistent, returns 0. If not consistent, returns a vector with a number of tests, where TRUE indicates a failed test.

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu

Change ggplot coordinates to plot radar - From package see

Description

Change ggplot coordinates to plot radar - From package see

Usage

coord_radar(theta = "x", start = 0, direction = 1)

Arguments

theta

ariable to map angle to (x or y)

start

offset of starting point from 12 o'clock in radians. Offset is applied clockwise or anticlockwise depending on value of direction.

direction

1, clockwise; -1, anticlockwise

Get effects information

Description

Get effects information

Usage

data_effects(
  qtl_info,
  effects,
  pheno.col = NULL,
  parents = NULL,
  lgs = NULL,
  groups = NULL,
  position = NULL,
  software,
  design = c("bar", "circle", "digenic")
)

Arguments

qtl_info

effects

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

pheno.col

integer identifying phenotype

parents

vector with parents ID

lgs

vector of integers with linkage group ID of selected QTL/s

groups

vector of integers with selected linkage group ID

position

vector of centimorgan positions of selected QTL/s

software

character defining which software was used for QTL analysis. Currently support for: QTLpoly, diaQTL and polyqtlR.

design

character defining the graphic design. Options: 'bar' - barplot of the effects; 'circle' - circular plot of the effects (useful to compare effects of different traits); 'digenic' - heatmap plotting sum of additive effects (bottom diagonal) and digenic effects (top diagonal) when present

Value

ggplot graphic

Returns the class with the highest probability in a genotype probability distribution. Function from MAPpoly.

Description

Returns the class with the highest probability in a genotype probability distribution. Function from MAPpoly.

Usage

dist_prob_to_class(geno, prob.thres = 0.9)

Arguments

geno

the probabilistic genotypes contained in the object 'mappoly.data'

prob.thres

probability threshold to select the genotype. Values below this genotype are assumed as missing data

Value

a matrix containing the doses of each genotype and marker. Markers are disposed in rows and individuals are disposed in columns. Missing data are represented by NAs

Draws linkage map, parents haplotypes and marker doses Adapted from MAPpoly

Description

Draws linkage map, parents haplotypes and marker doses Adapted from MAPpoly

Usage

draw_map_shiny(
  left.lim = 0,
  right.lim = 5,
  ch = 1,
  maps.dist,
  ph.p1,
  ph.p2,
  d.p1,
  d.p2,
  snp.names = TRUE,
  software = NULL
)

Arguments

left.lim

covered window in the linkage map start position

right.lim

covered window in the linkage map end position

ch

linkage group ID

ph.p1

list containing a data.frame for each group with parent 1 estimated phases. The data.frame contain the columns: 1) Character vector with chromosome ID; 2) Character vector with marker ID; 3 to (ploidy number)*2 columns with each parents haplotypes

ph.p2

list containing a data.frame for each group with parent 2 estimated phases. See ph.p1 parameter description.

d.p1

list containing a data.frame for each group with parent 1 dosages. The data.frame contain the columns: 1) character vector with chromosomes ID; 2) Character vector with markers ID; 3) Character vector with parent ID; 4) numerical vector with dosage

d.p2

list containing a data.frame for each group with parent 2 dosages. See d.p1 parameter description

snp.names

logical TRUE/FALSE. If TRUE it includes the marker names in the plot

software

character defined from each software it comes from

maps

list containing a vector for each linkage group markers with marker positions (named with marker names)

Value

graphic representing selected section of a linkage group

Filter non-conforming classes in F1, non double reduced population. Function from MAPpoly.

Description

Filter non-conforming classes in F1, non double reduced population. Function from MAPpoly.

Usage

filter_non_conforming_classes(input.data, prob.thres = NULL)

Arguments

input.data

object of class mappoly

prob.thres

threshold for filtering genotypes by genotype probability values. If NULL, the filter is not applied.

Value

filtered mappoly.data object

Extract the LOD Scores in a `'mappoly.map'` object Function from MAPpoly.

Description

Extract the LOD Scores in a 'mappoly.map' object Function from MAPpoly.

Usage

get_LOD(x, sorted = TRUE)

Arguments

x

an object of class mappoly.map

sorted

logical. if TRUE, the LOD Scores are displayed in a decreasing order

Value

a numeric vector containing the LOD Scores

Color pallet ggplot-like - Adapted from MAPpoly

Description

Color pallet ggplot-like - Adapted from MAPpoly

Usage

gg_color_hue(n)

Arguments

n

number of colors

Map functions - from MAPpoly

Description

Map functions - from MAPpoly

Usage

imf_h(r)

Arguments

r

vector with recombination fraction values

Value

vector with genetic distances

Import data from polymapR

Description

Function to import datasets from polymapR. Function from MAPpoly.

Usage

import_data_from_polymapR(
  input.data,
  ploidy,
  parent1 = "P1",
  parent2 = "P2",
  input.type = c("discrete", "probabilistic"),
  prob.thres = 0.95,
  pardose = NULL,
  offspring = NULL,
  filter.non.conforming = TRUE,
  verbose = TRUE
)

Arguments

input.data

a polymapR dataset

ploidy

the ploidy level

parent1

a character string containing the name (or pattern of genotype IDs) of parent 1

parent2

a character string containing the name (or pattern of genotype IDs) of parent 2

input.type

Indicates whether the input is discrete ("disc") or probabilistic ("prob")

prob.thres

threshold probability to assign a dosage to offspring. If the probability is smaller than thresh.parent.geno, the data point is converted to 'NA'.

pardose

matrix of dimensions (n.mrk x 3) containing the name of the markers in the first column, and the dosage of parents 1 and 2 in columns 2 and 3. (see polymapR vignette)

offspring

a character string containing the name (or pattern of genotype IDs) of the offspring individuals. If NULL (default) it considers all individuals as offsprings, except parent1 and parent2.

filter.non.conforming

if TRUE exclude samples with non expected genotypes under no double reduction. Since markers were already filtered in polymapR, the default is FALSE.

verbose

if TRUE (default), the current progress is shown; if FALSE, no output is produced

Details

See examples at https://rpubs.com/mmollin/tetra_mappoly_vignette.

Value

object of class mappoly.data

Author(s)

Marcelo Mollinari mmollin@ncsu.edu

References

Bourke PM et al: (2019) PolymapR — linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. _Bioinformatics_ 34:3496–3502. doi: 10.1093/bioinformatics/bty1002

Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378

Import phased map list from polymapR

Description

Function to import phased map lists from polymapR. Function from MAPpoly.

Usage

import_phased_maplist_from_polymapR(maplist, mappoly.data, ploidy = NULL)

Arguments

maplist

a list of phased maps obtained using function create_phased_maplist from package polymapR

mappoly.data

a dataset used to obtain maplist, converted into class mappoly.data

ploidy

the ploidy level

Details

See examples at https://rpubs.com/mmollin/tetra_mappoly_vignette.

Value

object of class mappoly.map

Author(s)

Marcelo Mollinari mmollin@ncsu.edu

References

Bourke PM et al: (2019) PolymapR — linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. _Bioinformatics_ 34:3496–3502. doi: 10.1093/bioinformatics/bty1002

Is it a probability dataset? Function from MAPpoly.

Description

Is it a probability dataset? Function from MAPpoly.

Usage

is.prob.data(x)

Arguments

x

object of class mappoly.data

Value

TRUE/FALSE indicating if genotype probability information is present

Gets summary information from map. Adapted from MAPpoly

Description

Gets summary information from map. Adapted from MAPpoly

Usage

map_summary(left.lim = 0, right.lim = 5, ch = 1, maps, d.p1, d.p2)

Arguments

left.lim

covered window in the linkage map start position

right.lim

covered window in the linkage map end position

ch

linkage group ID

maps

list containing a vector for each linkage group markers with marker positions (named with marker names)

d.p1

d.p2

list containing a data.frame for each group with parent 2 dosages. See d.p1 parameter description

Value

list with linkage map information: doses; number snps by group; cM per snp; map size; number of linkage groups

Haldane map function. From MAPpoly

Description

Haldane map function. From MAPpoly

Usage

mf_h(d)

Arguments

d

vector containing recombination fraction values

Value

vector with genetic distances estimated with Haldane function

Chi-square test. Function from MAPpoly.

Description

Chi-square test. Function from MAPpoly.

Usage

mrk_chisq_test(x, ploidy)

Arguments

x

data.frame containing dosage information

ploidy

integer defining the specie ploidy

Value

vector with p-values for each marker

Only the plot part of plot_profile function

Description

Only the plot part of plot_profile function

Usage

only_plot_profile(pl.in)

Arguments

pl.in

output object from plot_profile when plot == TRUE

Value

ggplot graphic with QTL significance profile

Linkage phase format conversion: list to matrix. Function from MAPpoly.

Description

This function converts linkage phase configurations from list to matrix form

Usage

ph_list_to_matrix(L, ploidy)

Arguments

L

a list of configuration phases

ploidy

ploidy level

Value

a matrix whose columns represent homologous chromosomes and the rows represent markers

Linkage phase format conversion: matrix to list. Function from MAPpoly.

Description

This function converts linkage phase configurations from matrix form to list

Usage

ph_matrix_to_list(M)

Arguments

M

matrix whose columns represent homologous chromosomes and the rows represent markers

Value

a list of linkage phase configurations

Plots mappoly.homoprob from MAPpoly

Description

Plots mappoly.homoprob from MAPpoly

Usage

## S3 method for class 'mappoly.homoprob'
plot(x, stack = FALSE, lg = NULL, ind = NULL, verbose = TRUE, ...)

Arguments

x

an object of class mappoly.homoprob

stack

logical. If TRUE, probability profiles of all homologues are stacked in the plot (default = FALSE)

lg

indicates which linkage group should be plotted. If NULL (default), it plots the first linkage group. If "all", it plots all linkage groups

ind

indicates which individuals should be plotted. It can be the position of the individuals in the dataset or it's name. If NULL (default), the function plots the first individual

verbose

if TRUE (default), the current progress is shown; if FALSE, no output is produced

...

unused arguments

Scatter plot relating linkage map and genomic positions

Description

Scatter plot relating linkage map and genomic positions

Usage

plot_cm_mb(viewmap, group, range.min, range.max)

Arguments

viewmap

object of class viewmap

group

selected group ID

range.min

minimum value of the selected position range

range.max

maximum value of the selected position range

Plot effects data

Description

Plot effects data

Usage

plot_effects(
  data_effects.obj,
  software,
  design = c("bar", "circle", "digenic")
)

Arguments

data_effects.obj

output of function data_effects

software

character defining which software was used for QTL analysis. Currently support for: QTLpoly, diaQTL and polyqtlR.

design

Plot a genetic map - Adapted from MAPpoly

Description

This function plots a genetic linkage map(s)

Usage

plot_map_list(viewmap, horiz = TRUE, col = "ggstyle", title = "Linkage group")

Arguments

viewmap

object of class viewmap

horiz

logical. If FALSE, the maps are plotted vertically with the first map to the left. If TRUE (default), the maps are plotted horizontally with the first at the bottom

col

a vector of colors for the bars or bar components (default = 'lightgrey') ggstyle produces maps using the default ggplot color palette

title

a title (string) for the maps (default = 'Linkage group')

Value

A data.frame object containing the name of the markers and their genetic position

Author(s)

Marcelo Mollinari, mmollin@ncsu.edu

Cristiane Taniguti, chtaniguti@tamu.edu

References

Plot a single linkage group with no phase - from MAPpoly

Description

Plot a single linkage group with no phase - from MAPpoly

Usage

plot_one_map(x, i = 0, horiz = FALSE, col = "lightgray")

Arguments

x

vector of genetic distances

i

margins size

horiz

logical TRUE/FALSE. If TRUE the map is plotted horizontally.

col

color pallete to be used

Logarithm of P-value (LOP) profile plots. Modified version of QTLpoly function.

Description

Plots profiled logarithm of score-based P-values (LOP) from individual or combined traits.

Usage

plot_profile(
  profile,
  qtl_info,
  selected_mks,
  pheno.col = NULL,
  lgs.id = NULL,
  by_range = TRUE,
  range.min = NULL,
  range.max = NULL,
  plot = TRUE,
  software = NULL
)

Arguments

profile

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

qtl_info

selected_mks

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

pheno.col

integer identifying phenotype

lgs.id

integer identifying linkage group

by_range

logical TRUE/FALSE. If TRUE range.min and range.max will set a colored window in the plot and the other positions will be gray. If FALSE, range.min and range.max is ignored

range.min

position in centimorgan defining the start of the colored window

range.max

position in centimorgan defining the end of the colored window

plot

logical TRUE/FALSE. If FALSE the function return a data.frame with information for only_plot_profile function. If TRUE, it returns a ggplot graphic.

software

character defining which software was used for QTL analysis. Currently support for: QTLpoly, diaQTL and polyqtlR.

Value

ggplot graphic (if plot == TRUE) or data.frame (if plot == FALSE) with information from QTL significance profile

Converts list of mappoly.map object into viewmap object

Description

Converts list of mappoly.map object into viewmap object

Usage

prepare_MAPpoly(mappoly_list)

Arguments

mappoly_list

list with objects of class mappoly.map

Value

object of class viewmap

Converts QTLpoly outputs to viewqtl object

Description

Converts QTLpoly outputs to viewqtl object

Usage

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

Arguments

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"

Value

object of class viewqtl

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu

Converts diaQTL output to viewqtl object

Description

Converts diaQTL output to viewqtl object

Usage

prepare_diaQTL(scan1_list, scan1_summaries_list, fitQTL_list, BayesCI_list)

Arguments

scan1_list

list with results from diaQTL scan1 function

scan1_summaries_list

list with results from diaQTL scan1_summaries function

fitQTL_list

list with results from diaQTL fitQTL function

BayesCI_list

list with results from diaQTL BayesCI function

Value

object of class viewqtl

Upload example files

Description

Upload example files

Usage

prepare_examples(example)

Arguments

example

character indicating the example dataset selected

Value

object of class viewpoly

Upload hidecan example files

Description

Upload hidecan example files

Usage

prepare_hidecan_examples(example)

Arguments

example

character indicating the example dataset selected

Value

object of class viewpoly

prepare maps for plot - from MAPpoly

Description

prepare maps for plot - from MAPpoly

Usage

prepare_map(input.map, config = "best")

Arguments

input.map

object of class mappoly.map

config

choose between 'best', 'all' or provide vector with defined configuration. 'best' provide just the best estimated configuration. 'all' provides all possibles.

Value

list containing phase and dosage information

Converts map information in custom format files to viewmap object

Description

Converts map information in custom format files to viewmap object

Usage

prepare_map_custom_files(dosages, phases, genetic_map, mks_pos = NULL)

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

mks_pos

TSV or TSV.GZ file with table with three columns: 1) marker ID; 2) genome position; 3) chromosome

Value

object of class viewmap

Converts polymapR ouputs to viewmap object

Description

Converts polymapR ouputs to viewmap object

Usage

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

Arguments

polymapR.dataset

a polymapR dataset

polymapR.map

output map sequence from polymapR

input.type

indicates whether the input is discrete ("disc") or probabilistic ("prob")

ploidy

ploidy level

Value

object of class viewmap

Converts polyqtlR outputs to viewqtl object

Description

Converts polyqtlR outputs to viewqtl object

Usage

prepare_polyqtlR(polyqtlR_QTLscan_list, polyqtlR_qtl_info, polyqtlR_effects)

Arguments

polyqtlR_QTLscan_list

list containing results from polyqtlR QTLscan_list function

polyqtlR_qtl_info

data.frame containing the QTL information:LG - group ID; Pos - QTL position (cM); pheno - phenotype ID; Pos_lower - lower position of confidence interval; Pos_upper - upper position of the confidence interval; thresh - LOD threshold applied

polyqtlR_effects

data.frame with results from visualiseQTLeffects polyqtlR function

Value

object of class viewqtl

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

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

Check hidecan inputs

Description

Check hidecan inputs

Usage

read_input_hidecan(input_list, func)

Arguments

input_list

shiny input result containing file path

func

hidecan read input function

Run the Shiny Application

Description

Run the Shiny Application

Usage

run_app(
  onStart = NULL,
  options = list(),
  enableBookmarking = NULL,
  uiPattern = "/",
  ...
)

Arguments

onStart

A function that will be called before the app is actually run. This is only needed for shinyAppObj, since in the shinyAppDir case, a global.R file can be used for this purpose.

options

Named options that should be passed to the runApp call (these can be any of the following: "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode"). You can also specify width and height parameters which provide a hint to the embedding environment about the ideal height/width for the app.

enableBookmarking

Can be one of "url", "server", or "disable". The default value, NULL, will respect the setting from any previous calls to enableBookmarking(). See enableBookmarking() for more information on bookmarking your app.

uiPattern

A regular expression that will be applied to each GET request to determine whether the ui should be used to handle the request. Note that the entire request path must match the regular expression in order for the match to be considered successful.

...

arguments to pass to golem_opts. See '?golem::get_golem_options' for more details.

Polysomic segregation frequency - Function from MAPpoly

Description

Computes the polysomic segregation frequency given a ploidy level and the dosage of the locus in both parents. It does not consider double reduction.

Usage

segreg_poly(ploidy, d.p1, d.p2)

Arguments

ploidy

the ploidy level

d.p1

the dosage in parent P

d.p2

the dosage in parent Q

Value

a vector containing the expected segregation frequency for all possible genotypic classes.

Author(s)

Marcelo Mollinari, mmollin@ncsu.edu

References

Serang O, Mollinari M, Garcia AAF (2012) Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids. _PLoS ONE_ 7(2): e30906.

Plot selected haplotypes

Description

Plot selected haplotypes

Usage

select_haplo(
  input.haplo,
  probs,
  selected_mks,
  effects.data,
  exclude.haplo = NULL
)

Arguments

input.haplo

character vector with selected haplotypes. It contains the information: "Trait:<trait ID>_LG:<linkage group ID_Pos:<QTL position>"

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

selected_mks

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

effects.data

output object from data_effects function

exclude.haplo

character vector with haplotypes to be excluded. It contains the information: "Trait:<trait ID>_LG:<linkage group ID_Pos:<QTL position>"

Value

ggplot graphic

Summary maps - adapted from MAPpoly

Description

This function generates a brief summary table

Usage

summary_maps(viewmap, software = NULL)

Arguments

viewmap

a list of objects of class viewmap

software

character defined from each software it comes from

Value

a data frame containing a brief summary of all maps

Author(s)

Gabriel Gesteira, gabrielgesteira@usp.br

Cristiane Taniguti, chtaniguti@tamu.edu

Estimate breeding values - Adapted function from QTLpoly

Description

Usage

Arguments

Value

Calculates homologues probabilities - Adapted from MAPpoly

Description

Usage

Arguments

Value

Viewmap object sanity check

Description

Usage

Arguments

Value

Author(s)

Viewpoly object sanity check

Description

Usage

Arguments

Value

Author(s)

viewqtl object sanity check

Description

Usage

Arguments

Value

Author(s)

Change ggplot coordinates to plot radar - From package see

Description

Usage

Arguments

Get effects information

Description

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Returns the class with the highest probability in a genotype probability distribution. Function from MAPpoly.

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Draws linkage map, parents haplotypes and marker doses Adapted from MAPpoly

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Filter non-conforming classes in F1, non double reduced population. Function from MAPpoly.

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Extract the LOD Scores in a 'mappoly.map' object Function from MAPpoly.

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Color pallet ggplot-like - Adapted from MAPpoly

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Map functions - from MAPpoly

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Import data from polymapR

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Import phased map list from polymapR

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Extract the LOD Scores in a `'mappoly.map'` object Function from MAPpoly.