qtl2

Collaborative Cross colors

Add thresholds to genome scan plot

Basic summaries of a cross2 object

Batch columns by pattern of missing values

Split vector into batches

Calculate Bayes credible intervals

Calculate entropy of genotype probability distribution

Calculate genotyping error LOD scores

Calculate genotype frequencies

Calculate conditional genotype probabilities

Calculate indicators of which marker/pseudomarker positions are along a fixed grid

Calculate heterozygosities

Calculate kinship matrix

Calculate founder minor allele frequencies from raw SNP genotypes

Calculate genotype frequencies from raw SNP genotypes

Calculate estimated heterozygosity from raw SNP genotypes

Calculate minor allele frequency from raw SNP genotypes

Calculate strain distribution pattern from SNP genotypes

Join genotype probabilities for different chromosomes

Join genome scan results for different phenotypes.

Combine columns from multiple scan1 permutation results

Join genotype imputations for different chromosomes

Join viterbi results for different chromosomes

Combine matrices by columns, expanding and aligning rows

Check a cross2 object

Chi-square test on all pairs of columns

Calculate chromosome lengths

Clean an object

Clean genotype probabilities

Clean scan1 output

Compare individuals' genotype data

Compare two sets of genotype probabilities

Compare two marker maps

Convert R/qtl cross object to new format

Count numbers of crossovers

Create a function to query genes

Create snp information table for a cross

Create a function to query variants

Calculate eigen decomposition of kinship matrix

Drop markers from a cross2 object

Drop markers with no genotype data

Estimate heritability with a linear mixed model

Estimate genetic maps

Find IBD segments for a set of strains

Find name of indexed snp

Find gaps in a genetic map

Find markers by chromosome position

Find positions of markers

Find peaks in a set of LOD curves

Fit single-QTL model at a single position

Convert genotype probabilities to allele probabilities

Convert genotype probabilities to SNP probabilities

Get common set of IDs from objects

Get X chromosome covariates

Guess phase of imputed genotypes

Create index of equivalent SNPs

Insert pseudomarkers into a marker map

Interpolate genotype probabilities

Interpolate between maps

Calculate SNP genotype matrix from strain distribution patterns

Locate crossovers

Calculate LOD support intervals

Subset a map to positions on a grid

Define strata based on rows of a matrix

Find pair with most similar genotypes

Find position with maximum LOD score

Overall maximum LOD score

Find genotypes with maximum marginal probabilities

Count missing genotypes

Plot QTL effects along chromosome

Plot of compare_geno object.

Plot gene locations for a genomic interval

Plot genotype probabilities for one individual on one chromosome.

Plot comparison of two sets of genotype probabilities

Plot LOD scores vs QTL peak locations

Plot one individual's genome-wide genotypes

Plot QTL peak locations

Plot phenotype vs genotype

Plot a genome scan

Plot SNP associations

Predict SNP genotypes

Print a cross2 object

Print summary of scan1perm permutations

Subset genotype probability array to pseudomarkers on a grid

Pull genotype probabilities for an interval

Pull genotype probabilities for a particular position

Drop all but a specified set of markers

Internal functions

qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Installed version of R/qtl2

Join genotype probabilities for different individuals

Join genome scan results for different chromosomes.

Combine data from scan1perm objects

Join genotype imputations for different individuals

Join Viterbi results for different individuals

Read QTL data from files

Read a csv file

Read a csv file that has numeric columns

Read phenotype data

Recode SNPs by major allele

Reduce the lengths of gaps in a map

Reduce markers to a subset of more-evenly-spaced ones

Replace individual IDs

Scale kinship matrix

Genome scan with a single-QTL model

Calculate BLUPs of QTL effects in scan along one chromosome

Calculate QTL effects in scan along one chromosome

Maximum LOD score from genome scan with a single-QTL model

Permutation test for genome scan with a single-QTL model

Single-QTL genome scan at imputed SNPs

Convert strain distribution patterns to character strings

Simulate genotypes given observed marker data

Subsetting genotype probabilities

Subsetting data for a QTL experiment

Subsetting imputed genotypes

Subsetting Viterbi results

Subset scan1 output

Summary of cross2 object

Basic summary of compare_geno object

Summarize scan1perm results

Create table of top snp associations

Calculate most probable sequence of genotypes

Write a control file for QTL data

Get x-axis position for genomic location

Zip a set of data files