Construction of Genetic Maps in Experimental Crosses
Perform gaussian sum
Creates a new sequence by adding markers.
Add the redundant markers removed by create_data_bins function
Calculates individual significance level to be used to achieve a globa...
Onemap object sanity check
Twopts object sanity check
Combine OneMap datasets
Compare all possible orders (exhaustive search) for a given sequence o...
New dataset based on bins
Create a dataframe suitable for a ggplot2 graphic
Create database and ggplot graphic of allele reads depths
Build genotype probabilities matrix for hmm
Draw a genetic map
Draw a linkage map
Creates a new sequence by dropping markers.
Edit sequence ordered by reference genome positions comparing to anoth...
Produce empty object to avoid code break. Function for internal purpos...
C++ routine for multipoint analysis in outcrossing populations
Export genotype probabilities in MAPpoly format (input for QTLpoly)
Export OneMap maps to be visualized in VIEWpoly
Extract allele counts of progeny and parents of vcf file
Filter markers based on 2pts distance
Filter markers according with a missing data threshold
Function filter genotypes by genotype probability
Allocate markers into bins
Function to divide the sequence in batches with user defined size
Assign markers to preexisting linkage groups
Assign markers to linkage groups
Assign markers to linkage groups
Apply Haldane mapping function
Keep in the onemap and twopts object only markers in the sequences
Apply Kosambi mapping function
Load list of sequences saved by save_onemap_sequences
Create a sequence of markers based on other OneMap object types
Repeat HMM if map find unlinked marker
Mapping overlapping batches
Perform map using background objects with only selected markers. It sa...
Construct the linkage map for a sequence of markers
Informs the segregation patterns of markers
OneMap interface with MDSMap package with option for multipoint distan...
Convert vcf file to onemap object
Order the markers in a sequence using the genomic position
Search for the best order of markers combining compare and try_seq fun...
Generates data.frame with parents estimated haplotypes
Picking optimal batch size values
Draw a graphic showing the number of markers of each segregation patte...
Draws a physical vs cM map
Show the results of grouping procedure
Plot recombination breakpoints counts for each individual
Plots progeny haplotypes
Plot p-values for chi-square tests of expected segregation
Draw a graphic of raw data for any OneMap population
print method for object class 'compare'
Show the results of grouping markers to preexisting sequence
Show the results of grouping procedure
Show the results of grouping procedure
print method for object class 'onemap_bin'
Show the results of segregation tests
Print method for object class 'onemap'
Print order_seq object
Print method for object class 'rf_2pts'
Print method for object class 'sequence'
Print method for object class 'try'
Plot number of breakpoints by individuals
Generate data.frame with genotypes estimated by HMM and its probabilit...
Rapid Chain Delineation
Read data from a Mapmaker raw file
Read data from all types of progenies supported by OneMap
Recombination Counting and Ordering
Remove individuals from the onemap object
Two-point analysis between genetic markers
Plots pairwise recombination fractions and LOD Scores in a heatmap
Filter markers according with a two-points recombination fraction and ...
Compares and displays plausible alternative orders for a given linkage...
Remove duplicated markers keeping the one with less missing data
Save a list of onemap sequence objects
Construct the linkage map for a sequence of markers after seeding phas...
Show markers with/without segregation distortion
Extract marker number by name
Seriation
Defines the default mapping function
Sort markers in onemap object by their position in reference genome
Split rf_2pts object by markers
Split onemap data sets
Suggests a LOD Score for two point tests
Create table with summary information about the linkage map
test_segregation_of_a_marker
test_segregation
Run try_seq considering previous sequence
Try to map a marker into every possible position between markers in a ...
Unidirectional Growth
These functions are defunct and no longer available.
Write a genetic map to a file
Convert onemap object to onemap raw file
Analysis of molecular marker data from model (backcrosses, F2 and recombinant inbred lines) and non-model systems (i. e. outcrossing species). For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu et al. (2002) <doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint approaches using hidden Markov models.
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