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 |
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 |