Linkage Analysis in Outcrossing Polyploids

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Documentation for package ‘polymapR’ version 1.0.16

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A B C D F G H I L M O P R S T V W

polymapR-package Linkage analysis in polyploids

-- A --

add_dup_markers Add duplicate markers to a map
ALL_dosages A dosage matrix for a random pairing tetraploid with five linkage groups.
all_linkages_list_P1 A (nested) list of linkage data frames classified per linkage group and homologue
all_linkages_list_P1_split A (nested) list of linkage data frames classified per linkage group and homologue
all_linkages_list_P1_subset A (nested) list of linkage data frames classified per linkage group and homologue
assembleDuplexLinks Use bridge markers to cluster homologues into linkage groups
assign_linkage_group Assign non-SN markers to a linkage group and homologue(s).
assign_SN_SN Assign (leftover) 1.0 markers

-- B --

bridgeHomologues Use bridge markers to cluster homologues into linkage groups

-- C --

calcPotShifts Calculate potential shifts in marker dosages
calcSegtypeInfo Build a list of segregation types
calc_binning_thresholds calc_binning_thresholds
calc_q1 calc_q1 ***********************************************************
calc_q2 calc_q2 ***********************************************************
calc_q3 calc_q3 ***********************************************************
calc_qall calc_qall ***********************************************************
checkF1 Identify the best-fitting F1 segregation types
checkFilename checkFilename ***********************************************************
check_map Check the quality of a linkage map using heatplots
check_marker_assignment Check for consistent marker assignment between both parents
chk2integer chk2integer ***********************************************************
cluster_per_LG Cluster 1.0 markers into correct homologues per linkage group
cluster_SN_markers Cluster 1.0 markers
colour.bar Add colour bar scale to heatplot
consensus_LG_assignment Consensus LG assignment
consensus_LG_names Find consensus linkage group names
convert_marker_dosages Convert marker dosages to the basic types.
correctDosages Check if dosage scores may have to be shifted
createChmHomList User interface for specifying linkage group for a homologue
createMap Marker ordering function
createTetraOriginInput Create input files for TetraOrigin using an integrated linkage map list and marker dosage matrix
create_phased_maplist Create a phased homologue map list using the original dosages

-- D --

define_LG_structure Generate linkage group and homologue structure of SxN markers
digamfrq digamfrq ***********************************************************

-- F --

finish_linkage_analysis Linkage analysis between all markertypes within LG.

-- G --

gcd gcd ***********************************************************
gcd_all gcd_all ***********************************************************
getConsensusGeno getConsensusGeno ***********************************************************
getMatchParents getMatchParents ***********************************************************
get_markertype_combinations Visualize and get all markertype combinations for which there are functions in polymapR

-- H --

homologue_lg_assignment Assign markers to linkage groups and homologues.

-- I --

integrated.maplist A nested list with integrated maps

-- L --

leftstr Get substrings from the lefthand side
LGHomDf_P1_1 A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker
LGHomDf_P2_1 A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker
LGHomDf_P2_2 A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker
linkage Calculate recombination frequency, LOD and phase
linterpol linterpol ***********************************************************

-- M --

makeProgeny makeProgeny ***********************************************************
maplist_P1 A list of maps of one parent
maplist_P1_subset A list of maps of one parent
maplist_P2_subset A list of maps of one parent
marker_assignments_P1 A 'data.frame' with marker assignments
marker_assignments_P2 A 'data.frame' with marker assignments
marker_binning Perform binning of markers.
marker_binning_list Bin markers that are in a nested list
marker_data_summary Summarize marker data
MDSMap_from_list Wrapper function for MDSMap to generate linkage maps from list of pairwise linkage estimates
merge_homologues Merge homologues
merge_marker_assignments Merge marker assignments
Mode Calculate the mode of a vector

-- O --

orient_and_merge_maps Align and integrate maps
overviewSNlinks Plotting 1.0 links between homologues

-- P --

P1_DxN_Assigned A 'data.frame' with marker assignments
P1_homologues A list of cluster stacks at different LOD scores
P1_SxS_Assigned A 'data.frame' with marker assignments
P2_DxN_Assigned A 'data.frame' with marker assignments
P2_homologues A list of cluster stacks at different LOD scores
P2_homologues_triploid A list of cluster stacks at different LOD scores
P2_SxS_Assigned A 'data.frame' with marker assignments
P2_SxS_Assigned_2 A 'data.frame' with marker assignments
p4_1.0_1.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.0_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.0_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.0_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.0_2.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.0_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.0_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.1_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.1_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.1_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.1_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.2_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.2_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.2_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.3_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.3_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.3_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_1.3_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_2.0_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_2.0_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_2.0_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_2.0_2.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_2.0_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_2.0_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_2.1_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_2.2_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p4_functions Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
p6_1.0_1.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
parental_quantities Calculate frequency of each markertype.
PCA_progeny Perform a PCA on progeny
phased.maplist A list of phased maps
phase_SN_diploid Phase 1.0 markers at the diploid level
plot_hom_vs_LG Plot homologue position versus integrated positions
plot_linkage_df Plot r versus LOD grouped by phase
plot_map Plot linkage maps
plot_phased_maplist Visualise the phased homologue maplist
plot_SNlinks Plot links between 1.0 markers
polygamfrq polygamfrq ***********************************************************
polymapR Linkage analysis in polyploids
prepare_pwd Prepare pwd for mapping scripts e.g. MDSmap

-- R --

r3_0.1_0.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_0.1_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_0.1_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_1.0_1.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_1.0_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_1.0_2.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_1.0_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_1.1_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_1.1_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_2.0_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_2.0_2.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_2.0_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_2.1_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_functions Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r4_1.0_1.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.0_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.0_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.0_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.0_2.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.0_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.0_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.1_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.1_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.1_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.1_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.2_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.2_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.2_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.3_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.3_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.3_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_1.3_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_2.0_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_2.0_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_2.0_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_2.0_2.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_2.0_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_2.1_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_2.1_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_2.2_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r4_functions Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r6_1.0_1.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_1.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_1.5 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_2.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_2.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_3.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_3.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_3.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.0_4.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_1.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_1.5 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_2.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_2.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_3.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.1_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_1.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_1.5 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_2.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_3.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_3.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_3.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.2_4.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.3_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.3_1.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.3_1.5 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.3_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.3_2.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.3_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.3_3.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.3_3.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.3_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.3_4.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.4_1.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.4_1.5 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.4_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.4_2.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.4_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.4_3.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.4_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.4_4.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.5_1.5 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.5_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.5_2.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.5_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.5_3.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_1.5_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_1.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_1.5 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_2.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_2.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_2.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_3.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_3.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_3.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.0_4.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.1_1.5 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.1_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.1_3.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.2_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.2_2.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.2_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.2_3.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.2_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.3_2.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.3_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.3_3.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.3_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_2.4_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_1.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_1.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_1.5 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_2.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_2.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_3.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_3.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_3.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.0_4.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.3_2.4 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_3.3_3.3 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
r6_functions Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
rightstr Get substrings from the righthand side
r_LOD_plot Plot r versus LOD

-- S --

screened_data A dosage matrix for a random pairing tetraploid with five linkage groups.
screened_data2 A dosage matrix for a random pairing tetraploid with five linkage groups.
screened_data3 A dosage matrix for a random pairing tetraploid with five linkage groups.
screen_for_duplicate_individuals Screen for duplicate individuals
screen_for_duplicate_markers Screen for and remove duplicated markers
screen_for_NA_values Screen marker data for NA values
segregating_data A dosage matrix for a random pairing tetraploid with five linkage groups.
segtypeInfoSummary Summarize the segtypeInfo list
selSegtypeInfo Restrict a list of segregation types to specified inheritance modes
SNSN_LOD_deviations Identify deviations in LOD scores between pairs of simplex x nulliplex markers
SN_DN_P1 A linkage 'data.frame'.
SN_DN_P2 A linkage 'data.frame'.
SN_SN_P1 A linkage 'data.frame'.
SN_SN_P2 A linkage 'data.frame'.
SN_SN_P2_triploid A linkage 'data.frame'.
SN_SS_P1 A linkage 'data.frame'.
SN_SS_P2 A linkage 'data.frame'.
split_linkage_info Split linkage information into homologues

-- T --

test_cluster_stack Error and warning handling for cluster_stack
test_dosage_matrix Error and warning handling for dosage_matrix
test_LG_hom_stack Error and warning handling for LG_hom_stack
test_linkage_df Error and warning handling for linkage_df
test_prefpairing Check for and estimate preferential pairing
TRI_dosages A dosage matrix for a random pairing tetraploid with five linkage groups.

-- V --

vector.to.matrix Large vector or in standardized matrix

-- W --

write.logheader Write a header for the log file
write.mct Write MapChart file
write.pwd Write a JoinMap compatible .pwd file from linkage data.frame.
write.TSNPM Write TetraploidSNPMap input file
write_nested_list Write out a nested list
write_pwd_list Write pwd files from a nested list