Calculate Bayes credible intervals
Calculate genotype frequencies from raw SNP genotypes
Join genotype probabilities for different chromosomes
Join genome scan results for different phenotypes.
Calculate heterozygosities
Calculate indicators of which marker/pseudomarker positions are along a fixed grid
Clean an object
Calculate chromosome lengths
Calculate estimated heterozygosity from raw SNP genotypes
Clean genotype probabilities
Batch columns by pattern of missing values
Calculate kinship matrix
Clean scan1 output
Basic summaries of a cross2 object
Calculate minor allele frequency from raw SNP genotypes
Check a cross2 object
Calculate strain distribution pattern from SNP genotypes
Chi-square test on all pairs of columns
Calculate founder minor allele frequencies from raw SNP genotypes
Combine columns from multiple scan1 permutation results
Create a function to query genes
Count numbers of crossovers
Find peaks in a set of LOD curves
Calculate eigen decomposition of kinship matrix
Join viterbi results for different chromosomes
Combine matrices by columns, expanding and aligning rows
Create snp information table for a cross
Drop markers from a cross2 object
create_variant_query_func
Create a function to query variants
Find markers by chromosome position
Find positions of markers
Find name of indexed snp
Insert pseudomarkers into a marker map
Convert genotype probabilities to allele probabilities
Convert genotype probabilities to SNP probabilities
Fit single-QTL model at a single position
Interpolate genotype probabilities
Find gaps in a genetic map
Compare individuals' genotype data
Count missing genotypes
Find pair with most similar genotypes
Find position with maximum LOD score
Join genotype imputations for different chromosomes
Compare two marker maps
Convert R/qtl cross object to new format
Plot QTL peak locations
Drop markers with no genotype data
Get common set of IDs from objects
Estimate heritability with a linear mixed model
Plot phenotype vs genotype
Internal functions
Compare two sets of genotype probabilities
qtl2: Quantitative Trait Locus Mapping in Experimental Crosses
Plot QTL effects along chromosome
Join genotype probabilities for different individuals
Installed version of R/qtl2
Subset genotype probability array to pseudomarkers on a grid
Plot a genome scan
Find IBD segments for a set of strains
Interpolate between maps
Estimate genetic maps
plot strain distribution patterns for SNPs
Pull genotype probabilities for an interval
Guess phase of imputed genotypes
Maximum LOD score from genome scan with a single-QTL model
Join genome scan results for different chromosomes.
Get X chromosome covariates
Permutation test for genome scan with a single-QTL model
Simulate genotypes given observed marker data
Overall maximum LOD score
Find genotypes with maximum marginal probabilities
Calculate LOD support intervals
Plot genotype probabilities for one individual on one chromosome.
Plot comparison of two sets of genotype probabilities
Locate crossovers
Create index of equivalent SNPs
Smooth genetic map
Combine data from scan1perm objects
Pull genotype probabilities for a particular position
Calculate SNP genotype matrix from strain distribution patterns
Calculate BLUPs of QTL effects in scan along one chromosome
Plot of compare_geno object.
Calculate QTL effects in scan along one chromosome
Subset a map to positions on a grid
Define strata based on rows of a matrix
Plot one individual's genome-wide genotypes
Print a cross2 object
Plot gene locations for a genomic interval
Plot LOD scores vs QTL peak locations
Calculate most probable sequence of genotypes
Subsetting Viterbi results
Subsetting imputed genotypes
Write a control file for QTL data
Drop all but a specified set of markers
Print summary of scan1perm permutations
Join Viterbi results for different individuals
Join genotype imputations for different individuals
Plot SNP associations
Read a csv file
Read QTL data from files
Read a csv file that has numeric columns
Reduce markers to a subset of more-evenly-spaced ones
Replace individual IDs
Predict SNP genotypes
Read phenotype data
Recode SNPs by major allele
Subset scan1 output
Genome scan with a single-QTL model
Scale kinship matrix
Summary of cross2 object
Convert strain distribution patterns to character strings
Single-QTL genome scan at imputed SNPs
Get x-axis position for genomic location
Subsetting genotype probabilities
Reduce the lengths of gaps in a map
Subsetting data for a QTL experiment
Zip a set of data files
Create table of top snp associations
Unsmooth genetic map
Basic summary of compare_geno object
Summarize scan1perm results
Calculate entropy of genotype probability distribution
Calculate genotype frequencies
Add thresholds to genome scan plot
Split vector into batches
Collaborative Cross colors
Calculate conditional genotype probabilities
Calculate genotyping error LOD scores