Create database and ggplot graphic of allele reads depths
C++ routine for multipoint analysis in outcrossing populations
Creates a new sequence by dropping markers.
Build genotype probabilities matrix for hmm
Filter markers according with a missing data threshold
Extract allele counts of progeny and parents of vcf file
Filter markers based on 2pts distance
Produce empty object to avoid code break. Function for internal purpose.
Draw a genetic map
Draw a linkage map
Assign markers to linkage groups
generate_overlapping_batches
Function to divide the sequence in batches with user defined size
Assign markers to linkage groups
Function filter genotypes by genotype probability
Allocate markers into bins
Apply Haldane mapping function
Assign markers to preexisting linkage groups
Keep in the onemap and twopts object only markers in the sequences
Apply Kosambi mapping function
Create a sequence of markers based on other OneMap object types
Simulated data from a F2 population
Data from a full-sib family derived from two outbred parents
Repeat HMM if map find unlinked marker
Construct the linkage map for a sequence of markers
Informs the segregation patterns of markers
Simulated data from a F2 population
Search for the best order of markers combining compare and try_seq
functions
Generates data.frame with parents estimated haplotypes
OneMap interface with MDSMap package with option for multipoint distances estimation
plot.onemap_progeny_haplotypes_counts
Plot recombination breakpoints counts for each individual
Draw a graphic of raw data for any OneMap population
Plot p-values for chi-square tests of expected segregation
plot.onemap_progeny_haplotypes
Plots progeny haplotypes
Simulated data from a backcross population
Show the results of grouping procedure
Show the results of grouping procedure
Print order_seq object
Show the results of grouping markers to preexisting sequence
Print method for object class 'onemap'
Print method for object class 'rf_2pts'
Generate data.frame with genotypes estimated by HMM and its probabilities
progeny_haplotypes_counts
Plot number of breakpoints by individuals
Simulated data from a RIL population produced by selfing.
Convert vcf file to onemap object
Perform map using background objects with only selected markers. It saves ram memory during the procedure.
It is useful if dealing with many markers in total data set.
print method for object class 'onemap_bin'
Show the results of segregation tests
Mapping overlapping batches
print method for object class 'compare'
Print method for object class 'sequence'
Draw a graphic showing the number of markers of each segregation pattern.
Picking optimal batch size values
Show the results of grouping procedure
Print method for object class 'try'
Recombination Counting and Ordering
Construct the linkage map for a sequence of markers after seeding phases
Read data from all types of progenies supported by OneMap
Show markers with/without segregation distortion
Rapid Chain Delineation
Extract marker number by name
Read data from a Mapmaker raw file
Defines the default mapping function
Compares and displays plausible alternative orders for a given linkage
group
Data generated from VCF file with biallelic markers from a f2 backcross population
These functions are defunct and no longer available.
Try to map a marker into every possible position between markers
in a given map
test_segregation_of_a_marker
test_segregation_of_a_marker
Split rf_2pts object by markers
Remove duplicated markers keeping the one with less missing data
Sort markers in onemap object by their position in reference genome
Split onemap data sets
Data generated from VCF file with biallelic markers from a f2 intercross population
Seriation
Run try_seq considering previous sequence
Remove individuals from the onemap object
Filter markers according with a two-points recombination fraction and LOD threshold. Adapted from MAPpoly.
Two-point analysis between genetic markers
Data generated from VCF file with biallelic markers from a full-sib family derived from two outbred parents
Unidirectional Growth
Plots pairwise recombination fractions and LOD Scores in a heatmap
Data generated from VCF file with biallelic markers from a RIL population produced by selfing
Write a genetic map to a file
Suggests a LOD Score for two point tests
test_segregation
Convert onemap object to onemap raw file
create_dataframe_for_plot_outcross
Create a dataframe suitable for a ggplot2 graphic
Compare all possible orders (exhaustive search) for a given sequence of
markers
Combine OneMap datasets
Calculates individual significance level to be used to achieve a global alpha (with Bonferroni)
Perform gaussian sum
Creates a new sequence by adding markers.
New dataset based on bins
Add the redundant markers removed by create_data_bins function
Onemap object sanity check
Twopts object sanity check