Linkage Analysis in Outcrossing Polyploids

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Documentation for package ‘polymapR’ version 1.1.6

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

-- A --

add_dup_markers Add back duplicate markers after mapping
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 --

calcSegtypeInfo Build a list of segregation types
checkF1 Identify the best-fitting F1 segregation types
check_map Check the quality of a linkage map
check_marker_assignment Check for consistent marker assignment between both parents
check_maxP check your dataset's maxP distribution
chk1 Example output of the checkF1 function
cluster_per_LG Cluster 1.0 markers into correct homologues per linkage group
cluster_SN_markers Cluster 1.0 markers
compare_maps Compare linkage maps, showing links between connecting markers common to neighbouring maps
consensus_LG_assignment Consensus LG assignment
consensus_LG_names Find consensus linkage group names
convert_marker_dosages Convert marker dosages to the basic types.
convert_polyRAD Convert (probabilistic) genotype calling results from polyRAD to input compatible with polymapR
convert_updog Convert (probabilistic) genotype calling results from updog to input compatible with polymapR.
correctDosages Check if dosage scores may have to be shifted
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

-- E --

exampleRAD_mapping Example output dataset of polyRAD::PipelineMapping2Parents function

-- F --

finish_linkage_analysis Linkage analysis between all markertypes within a linkage group.

-- G --

get_markertype_combinations Visualize and get all markertype combinations for which there are functions in polymapR
gp_df An example of a genotype probability data frame
gp_overview gp_overview
gp_vignette_data A list of objects needed to build the probabilistic genotype vignette

-- H --

homologue_lg_assignment Assign markers to linkage groups and homologues.

-- I --

integrated.maplist A nested list with integrated maps

-- L --

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
linkage.gp Calculate recombination frequency, LOD and phase using genotype probabilities

-- M --

map1 A sample map
map2 A sample map
map3 A sample map
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_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
mout Example output dataset of updog::multidog function

-- O --

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_functions Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
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_map Plot linkage maps
plot_phased_maplist Visualise the phased homologue maplist

-- R --

r2_1.0_1.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.
r2_1.0_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.
r2_1.1_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.
r2_functions Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.
r3_2_1.0_1.0 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.
r3_2_1.0_1.1 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.
r3_2_1.0_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.
r3_2_1.2_1.2 Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.
r3_functions Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.
r4_functions Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
r6_functions Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
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_individuals.gp Screen for duplicate individuals using weighted genotype probabilities
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.
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'.

-- T --

test_prefpairing Check for and estimate preferential pairing
TRI_dosages A dosage matrix for a random pairing tetraploid with five linkage groups.

-- W --

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