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