add_marker |
Add a single marker to a map |
cache_counts_twopt |
Frequency of genotypes for two-point recombination fraction estimation |
calc_genoprob |
Compute conditional probabilities of the genotypes |
calc_genoprob_dist |
Compute conditional probabilities of the genotypes using probability distribution of dosages |
calc_genoprob_error |
Compute conditional probabilities of the genotypes using global error |
calc_genoprob_single_parent |
Compute conditional probabilities of the genotype (one informative parent) |
calc_homologprob |
Homolog probabilities |
calc_prefpair_profiles |
Preferential pairing profiles |
check_data_sanity |
Data sanity check |
compare_maps |
Compare a list of maps |
cross_simulate |
Simulate an autopolyploid full-sib population |
detect_info_par |
Detects which parent is informative |
drop_marker |
Remove markers from a map |
edit_order |
Edit sequence ordered by reference genome positions comparing to another set order |
elim_redundant |
Eliminate redundant markers |
est_full_hmm_with_global_error |
Re-estimate genetic map given a global genotyping error |
est_full_hmm_with_prior_prob |
Re-estimate genetic map using dosage prior probability distribution |
est_pairwise_rf |
Pairwise two-point analysis |
est_pairwise_rf2 |
Pairwise two-point analysis - RcppParallel version |
est_rf_hmm |
Multipoint analysis using Hidden Markov Models in autopolyploids |
est_rf_hmm_sequential |
Multipoint analysis using Hidden Markov Models: Sequential phase elimination |
export_data_to_polymapR |
Export data to 'polymapR' |
export_map_list |
Export a genetic map to a CSV file |
export_qtlpoly |
Export to QTLpoly |
extract_map |
Extract the maker position from an object of class 'mappoly.map' |
filter_aneuploid |
Filter aneuploid chromosomes from progeny individuals |
filter_individuals |
Filter out individuals |
filter_missing |
Filter missing genotypes |
filter_segregation |
Filter markers based on chi-square test |
find_blocks |
Allocate markers into linkage blocks |
framework_map |
Design linkage map framework in two steps: i) estimating the recombination fraction with HMM approach for each parent separately using only markers segregating individually (e.g. map 1 - P1:3 x P2:0, P1: 2x4; map 2 - P1:0 x P2:3, P1:4 x P2:2); ii) merging both maps and re-estimate recombination fractions. |
genetic-mapping-functions |
Genetic Mapping Functions |
get_genomic_order |
Get the genomic position of markers in a sequence |
get_submap |
Extract sub-map from map |
get_tab_mrks |
Get table of dosage combinations |
group_mappoly |
Assign markers to linkage groups |
hexafake |
Simulated autohexaploid dataset. |
hexafake.geno.dist |
Simulated autohexaploid dataset with genotype probabilities. |
imf_h |
Genetic Mapping Functions |
imf_k |
Genetic Mapping Functions |
imf_m |
Genetic Mapping Functions |
import_data_from_polymapR |
Import data from polymapR |
import_from_updog |
Import from updog |
import_phased_maplist_from_polymapR |
Import phased map list from polymapR |
loglike_hmm |
Multipoint log-likelihood computation |
make_mat_mappoly |
Subset recombination fraction matrices |
make_pairs_mappoly |
Subset pairwise recombination fractions |
make_seq_mappoly |
Create a Sequence of Markers |
maps.hexafake |
Resulting maps from 'hexafake' |
mds_mappoly |
Estimates loci position using Multidimensional Scaling |
merge_datasets |
Merge datasets |
merge_maps |
Merge two maps |
mf_h |
Genetic Mapping Functions |
mf_k |
Genetic Mapping Functions |
mf_m |
Genetic Mapping Functions |
plot.mappoly.data |
Data Input |
plot.mappoly.geno.ord |
Get the genomic position of markers in a sequence |
plot.mappoly.homoprob |
Plots mappoly.homoprob |
plot.mappoly.map |
Multipoint analysis using Hidden Markov Models in autopolyploids |
plot.mappoly.prefpair.profiles |
Plots mappoly.prefpair.profiles |
plot.mappoly.rf.matrix |
Recombination fraction list to matrix |
plot.mappoly.sequence |
Create a Sequence of Markers |
plot_genome_vs_map |
Physical versus genetic distance |
plot_GIC |
Genotypic information content |
plot_mappoly.map2 |
Plot object mappoly.map2 |
plot_map_list |
Plot a genetic map |
plot_mrk_info |
Plot marker information |
plot_progeny_dosage_change |
Display genotypes imputed or changed by the HMM chain given a global genotypic error |
print.mappoly.data |
Data Input |
print.mappoly.geno.ord |
Get the genomic position of markers in a sequence |
print.mappoly.map |
Multipoint analysis using Hidden Markov Models in autopolyploids |
print.mappoly.pcmap |
Estimates loci position using Multidimensional Scaling |
print.mappoly.pcmap3d |
Estimates loci position using Multidimensional Scaling |
print.mappoly.rf.matrix |
Recombination fraction list to matrix |
print.mappoly.sequence |
Create a Sequence of Markers |
print_mrk |
Summary of a set of markers |
read_fitpoly |
Data Input in fitPoly format |
read_geno |
Data Input |
read_geno_csv |
Data Input in CSV format |
read_geno_prob |
Data Input |
read_vcf |
Data Input VCF |
reest_rf |
Re-estimate the recombination fractions in a genetic map |
rev_map |
Reverse map |
rf_list_to_matrix |
Recombination fraction list to matrix |
rf_snp_filter |
Remove markers that do not meet a LOD criteria |
segreg_poly |
Polysomic segregation frequency |
sim_homologous |
Simulate homology groups |
solcap.dose.map |
Resulting maps from 'tetra.solcap' |
solcap.err.map |
Resulting maps from 'tetra.solcap' |
solcap.mds.map |
Resulting maps from 'tetra.solcap' |
solcap.prior.map |
Resulting maps from 'tetra.solcap.geno.dist' |
split_and_rephase |
Divides map in sub-maps and re-phase them |
summary_maps |
Summary maps |
tetra.solcap |
Autotetraploid potato dataset. |
tetra.solcap.geno.dist |
Autotetraploid potato dataset with genotype probabilities. |
update_framework_map |
Add markers that are informative in both parents using HMM approach and evaluating difference in LOD and gap size |
update_map |
Update map |