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