polymapR-package |
Linkage analysis in polyploids |
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 |
bridgeHomologues |
Use bridge markers to cluster homologues into linkage groups |
calcSegtypeInfo |
Build a list of segregation types |
checkF1 |
Identify the best-fitting F1 segregation types |
check_map |
Check the quality of a linkage map using heatplots |
check_marker_assignment |
Check for consistent marker assignment between both parents |
cluster_per_LG |
Cluster 1.0 markers into correct homologues per linkage group |
cluster_SN_markers |
Cluster 1.0 markers |
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 |
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 |
define_LG_structure |
Generate linkage group and homologue structure of SxN markers |
finish_linkage_analysis |
Linkage analysis between all markertypes within LG. |
get_markertype_combinations |
Visualize and get all markertype combinations for which there are functions in polymapR |
homologue_lg_assignment |
Assign markers to linkage groups and homologues. |
integrated.maplist |
A nested list with integrated maps |
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 |
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 |
orient_and_merge_maps |
Align and integrate maps |
overviewSNlinks |
Plotting 1.0 links between homologues |
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_linkage_df |
Plot r versus LOD grouped by phase |
plot_map |
Plot linkage maps |
plot_phased_maplist |
Visualise the phased homologue maplist |
polymapR |
Linkage analysis in polyploids |
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_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_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_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 |
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. |
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 |
test_prefpairing |
Check for and estimate preferential pairing |
TRI_dosages |
A dosage matrix for a random pairing tetraploid with five linkage groups. |
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 |