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