qtl2 package - RDocumentation

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R/qtl2

R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software R/qtl, to better handle high-dimensional data and complex cross designs.

Also see the related packages, qtl2convert (for converting data among the R/qtl2, DOQTL, and R/qtl formats), qtl2fst (for storing genotype probabilities on disk), and qtl2ggplot (for ggplot2-based data visualizations).

Installation

Install R/qtl2 from CRAN:

install.packages("qtl2")

Documentation

Citation

To cite R/qtl2 in publications, use:

Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2019) R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations. Genetics 211:495-502 doi:10.1534/genetics.118.301595

License

Licensed under GPL-3.

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Version

Install

install.packages('qtl2')

Monthly Downloads

581

Version

0.40

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/rqtl/qtl2

Homepage

https://kbroman.org/qtl2/

Maintainer

Karl Broman

Last Published

May 4th, 2026

Functions in qtl2 (0.40)

Calculate chromosome lengths

Clean genotype probabilities

Join viterbi results for different chromosomes

Combine matrices by columns, expanding and aligning rows

Join genotype imputations for different chromosomes

Clean scan1 output

Check a cross2 object

Chi-square test on all pairs of columns

cbind.scan1perm

Combine columns from multiple scan1 permutation results

Create snp information table for a cross

Compare two marker maps

create_gene_query_func

Create a function to query genes

Clean an object

compare_genoprob

Compare two sets of genotype probabilities

Count numbers of crossovers

Convert R/qtl cross object to new format

create_variant_query_func

Create a function to query variants

Calculate eigen decomposition of kinship matrix

Compare individuals' genotype data

compare_founder_geno

Compare founders genotype data

Drop markers from a cross2 object

Find gaps in a genetic map

Find name of indexed snp

Find markers by chromosome position

drop_nullmarkers

Drop markers with no genotype data

Estimate heritability with a linear mixed model

Find positions of markers

find_ibd_segments

Find IBD segments for a set of strains

Estimate genetic maps

find_dup_markers

Find markers with identical genotype data

Create index of equivalent SNPs

fread_csv_numer

Read a csv file that has numeric columns

Get common set of IDs from objects

Find peaks in a set of LOD curves

genoprob_to_alleleprob

Convert genotype probabilities to allele probabilities

genoprob_to_snpprob

Convert genotype probabilities to SNP probabilities

Read a csv file

Fit single-QTL model at a single position

Get X chromosome covariates

Guess phase of imputed genotypes

Find position with maximum LOD score

Define strata based on rows of a matrix

insert_pseudomarkers

Insert pseudomarkers into a marker map

max_compare_geno

Find pair with most similar genotypes

Subset a map to positions on a grid

interp_genoprob

Interpolate genotype probabilities

Locate crossovers

Calculate LOD support intervals

Interpolate between maps

Calculate SNP genotype matrix from strain distribution patterns

Overall maximum LOD score

Effect plot with multiple CIs for different groups

Count missing genotypes

Plot QTL effects along chromosome

plot_genoprobcomp

Plot comparison of two sets of genotype probabilities

Plot genotype probabilities for one individual on one chromosome.

Find genotypes with maximum marginal probabilities

Plot LOD scores vs QTL peak locations

plot_compare_geno

Plot of compare_geno object.

Plot gene locations for a genomic interval

Plot QTL peak locations

Plot phenotype vs genotype

Plot one individual's genome-wide genotypes

Plot a genome scan

Plot SNP associations

print.summary.scan1perm

Print summary of scan1perm permutations

Print a cross2 object

predict_snpgeno

Predict SNP genotypes

Subset genotype probability array to pseudomarkers on a grid

pull_genoprobint

Pull genotype probabilities for an interval

pull_genoprobpos

Pull genotype probabilities for a particular position

Drop all but a specified set of markers

rbind.scan1perm

Combine data from scan1perm objects

Join genotype imputations for different individuals

Installed version of R/qtl2

plot strain distribution patterns for SNPs

Join genome scan results for different chromosomes.

rbind.calc_genoprob

Join genotype probabilities for different individuals

Replace individual IDs

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

Join Viterbi results for different individuals

reduce_map_gaps

Reduce the lengths of gaps in a map

Read phenotype data

align_scan1_map

Internal functions

Calculate BLUPs of QTL effects in scan along one chromosome

Genome scan with a single-QTL model

Recode SNPs by major allele

Read QTL data from files

Scale kinship matrix

qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Single-QTL genome scan at imputed SNPs

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

Calculate QTL effects in scan along one chromosome

Smooth genetic map

Simulate genotypes given observed marker data

Subsetting data for a QTL experiment

subset.calc_genoprob

Subsetting genotype probabilities

Convert strain distribution patterns to character strings

subset.sim_geno

Subsetting imputed genotypes

Permutation test for genome scan with a single-QTL model

summary_scan1perm

Summarize scan1perm results

summary_compare_geno

Basic summary of compare_geno object

Summary of cross2 object

Calculate most probable sequence of genotypes

Create table of top snp associations

Subset scan1 output

Subsetting Viterbi results

write_control_file

Write a control file for QTL data

Get x-axis position for genomic location

Zip a set of data files

Unsmooth genetic map

Batch columns by pattern of missing values

Calculate Bayes credible intervals

Split vector into batches

Collaborative Cross colors

Add thresholds to genome scan plot

Calculate genotype frequencies

Calculate entropy of genotype probability distribution

basic_summaries

Basic summaries of a cross2 object

Calculate genotyping error LOD scores

Join genome scan results for different phenotypes.

calc_raw_founder_maf

Calculate founder minor allele frequencies from raw SNP genotypes

Calculate conditional genotype probabilities

cbind.calc_genoprob

Join genotype probabilities for different chromosomes

Calculate heterozygosities

Calculate strain distribution pattern from SNP genotypes

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

Calculate minor allele frequency from raw SNP genotypes

calc_raw_geno_freq

Calculate genotype frequencies from raw SNP genotypes

Calculate estimated heterozygosity from raw SNP genotypes

Calculate kinship matrix