Genetic Linkage Maps in Autopolyploids
Add a single marker to a map
Add markers to a pre-existing sequence using HMM analysis and evaluati...
add a single marker at the tail of a linkage phase list
Aggregate matrix cells (lower the resolution by a factor)
Frequency of genotypes for two-point recombination fraction estimation
Compute conditional probabilities of the genotypes
Compute conditional probabilities of the genotypes using probability d...
Compute conditional probabilities of the genotypes using global error
Compute conditional probabilities of the genotypes given a sequence of...
Compute conditional probabilities of the genotype (one informative par...
Homolog probabilities
Preferential pairing profiles
cat for phase information
Checks the consistency of dataset (probability distribution)
Checks the consistency of dataset (dosage)
Data sanity check
Check if it is possible to estimate the recombination fraction between...
Compare a list of linkage phases and return the markers for which they...
Check if all pairwise combinations of elements of input.seqare conta...
Compare two polyploid haplotypes stored in list format
Compare a list of maps
Concatenate new marker
concatenate two linkage phase lists
Create a map with pseudomarkers at a given step
Simulate an autopolyploid full-sib population
Detects which parent is informative
Returns the class with the highest probability in a genotype probabili...
Draw simple parental linkage phase configurations
Plot the linkage phase configuration given a list of homologous chromo...
Remove markers from a map
Edit sequence ordered by reference genome positions comparing to anoth...
Eliminate configurations using two-point information
Eliminates equivalent linkage phase configurations
Eliminate redundant markers
Re-estimate genetic map given a global genotyping error
Re-estimate genetic map using dosage prior probability distribution
Estimate a genetic map given a sequence of block markers
Estimate a genetic map given a sequence of block markers given the con...
Pairwise two-point analysis
Pairwise two-point analysis - RcppParallel version
Multipoint analysis using Hidden Markov Models in autopolyploids
Multipoint analysis using Hidden Markov Models: Sequential phase elimi...
Multipoint analysis using Hidden Markov Models (single phase)
Multilocus analysis using Hidden Markov Models (single parent, single ...
Export data to polymapR
Export a genetic map to a CSV file
Export to QTLpoly
Extract the maker position from an object of class 'mappoly.map'
Filter aneuploid chromosomes from progeny individuals
Filter out individuals
Filter MAPpoly Map Configurations by Loglikelihood Threshold
Filter missing genotypes
Filter individuals based on missing genotypes
Filter markers based on missing genotypes
Filter non-conforming classes in F1, non double reduced population.
Filter markers based on chi-square test
Allocate markers into linkage blocks
Format results from pairwise two-point estimation in C++
Design linkage map framework in two steps: i) estimating the recombina...
Generate all possible linkage phases in matrix form given the dose and...
Eliminate equivalent linkage phases
Genetic Mapping Functions
Prior probability for genotyping error
Access a remote server to get Counts for recombinant classes
Counts for recombinant classes
Counts for recombinant classes
Counts for recombinant classes in a polyploid parent.
Counts for recombinant classes
Get Dosage Type in a Sequence
Get the tail of a marker sequence up to the point where the markers pr...
Get the genomic position of markers in a sequence
Given a pair of character indicating the numbers i and j : 'i-j', retu...
Get the indices of selected linkage phases given a threshold
Extract the LOD Scores in a 'mappoly.map' object
Get weighted ordinary least squared map give a sequence and rf matrix
Given a homology group in matrix form, it returns the number shared ho...
subset of a linkage phase list
Get the recombination fraction for a sequence of markers given an obje...
Get recombination fraction from a matrix
Get states and emission in one informative parent
Extract sub-map from map
Get table of dosage combinations
Get the number of bivalent configurations
Color pallet ggplot-like
Assign markers to linkage groups
Simulated autohexaploid dataset with genotype probabilities.
Simulated autohexaploid dataset.
Import data from polymapR
Import from updog
Import phased map list from polymapR
Check if Object is a Probability Dataset in MAPpoly
Multipoint log-likelihood computation
List of linkage phases
Subset recombination fraction matrices
Subset pairwise recombination fractions
Create a Sequence of Markers
MAPpoly Color Palettes
Resulting maps from hexafake
Estimates loci position using Multidimensional Scaling
Merge datasets
Merge two maps
Build merged parental maps
Chi-square test
Msg function
Parallel Pairwise Discrete Estimation
Wrapper function to discrete-based pairwise two-point estimation in C+...
Parallel Pairwise Probability Estimation
Auxiliary function to estimate a map in a block of markers using paral...
N!/2 combination
N! combination
Linkage phase format conversion: list to matrix
Linkage phase format conversion: matrix to list
Plots mappoly.homoprob
Plots mappoly.prefpair.profiles
Plot Two Overlapped Haplotypes
Physical versus genetic distance
Genotypic information content
Plot a genetic map
Plot object mappoly.map2
Plot marker information
plot a single linkage group with no phase
Display genotypes imputed or changed by the HMM chain given a global g...
Estimate genetic map using as input the probability distribution of ge...
prepare maps for plot
Summary of a set of markers
cat for graphical representation of the phases
Data Input in fitPoly format
Data Input
Data Input in CSV format
Data Input
Data Input VCF
Re-estimate the recombination fractions in a genetic map
Reverse map
Recombination fraction list to matrix
Remove markers that do not meet a LOD criteria
Random sampling of dataset
Polysomic segregation frequency
Select rf and lod based on thresholds
Simulate mapping population (one parent)
Simulate mapping population (tow parents)
Simulate homology groups
Resulting maps from tetra.solcap
Resulting maps from tetra.solcap
Resulting maps from tetra.solcap
Resulting maps from tetra.solcap.geno.dist
Divides map in sub-maps and re-phase them
Split map into sub maps given a gap threshold
Summary maps
Conversion of data.frame to mappoly.data
Autotetraploid potato dataset with genotype probabilities.
Autotetraploid potato dataset.
Add markers that are informative in both parents using HMM approach an...
Update map
Update missing information
makes a phase list from map, selecting only configurations under a cer...
Conversion: vector to matrix
Construction of genetic maps in autopolyploid full-sib populations. Uses pairwise recombination fraction estimation as the first source of information to sequentially position allelic variants in specific homologous chromosomes. For situations where pairwise analysis has limited power, the algorithm relies on the multilocus likelihood obtained through a hidden Markov model (HMM). For more detail, please see Mollinari and Garcia (2019) <doi:10.1534/g3.119.400378> and Mollinari et al. (2020) <doi:10.1534/g3.119.400620>.