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

676

Version

0.38

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/rqtl/qtl2

Homepage

https://kbroman.org/qtl2/

Maintainer

Karl Broman

Last Published

June 2nd, 2025

Functions in qtl2 (0.38)

calc_raw_geno_freq

Calculate genotype frequencies from raw SNP genotypes

Check a cross2 object

Join viterbi results for different chromosomes

Clean scan1 output

Clean genotype probabilities

Chi-square test on all pairs of columns

Calculate eigen decomposition of kinship matrix

create_variant_query_func

Create a function to query variants

Count numbers of crossovers

Convert R/qtl cross object to new format

create_gene_query_func

Create a function to query genes

Combine matrices by columns, expanding and aligning rows

Create snp information table for a cross

Join genotype imputations for different chromosomes

Join genome scan results for different phenotypes.

Compare individuals' genotype data

cbind.scan1perm

Combine columns from multiple scan1 permutation results

Find markers by chromosome position

Find positions of markers

compare_founder_geno

Compare founders genotype data

Find name of indexed snp

drop_nullmarkers

Drop markers with no genotype data

Drop markers from a cross2 object

Estimate heritability with a linear mixed model

Estimate genetic maps

genoprob_to_snpprob

Convert genotype probabilities to SNP probabilities

genoprob_to_alleleprob

Convert genotype probabilities to allele probabilities

Create index of equivalent SNPs

Guess phase of imputed genotypes

Get X chromosome covariates

Get common set of IDs from objects

fread_csv_numer

Read a csv file that has numeric columns

max_compare_geno

Find pair with most similar genotypes

Read a csv file

Find position with maximum LOD score

Calculate LOD support intervals

Locate crossovers

find_dup_markers

Find markers with identical genotype data

Compare two marker maps

Calculate chromosome lengths

Clean an object

compare_genoprob

Compare two sets of genotype probabilities

interp_genoprob

Interpolate genotype probabilities

Fit single-QTL model at a single position

Find peaks in a set of LOD curves

find_ibd_segments

Find IBD segments for a set of strains

Count missing genotypes

insert_pseudomarkers

Insert pseudomarkers into a marker map

Plot LOD scores vs QTL peak locations

Plot QTL effects along chromosome

plot_compare_geno

Plot of compare_geno object.

Find gaps in a genetic map

predict_snpgeno

Predict SNP genotypes

Plot SNP associations

Plot gene locations for a genomic interval

Find genotypes with maximum marginal probabilities

Overall maximum LOD score

Plot phenotype vs genotype

Plot QTL peak locations

Plot one individual's genome-wide genotypes

qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

align_scan1_map

Internal functions

pull_genoprobint

Pull genotype probabilities for an interval

pull_genoprobpos

Pull genotype probabilities for a particular position

Interpolate between maps

Subset genotype probability array to pseudomarkers on a grid

Calculate SNP genotype matrix from strain distribution patterns

Plot a genome scan

Define strata based on rows of a matrix

Subset a map to positions on a grid

plot strain distribution patterns for SNPs

Join genome scan results for different chromosomes.

Read QTL data from files

rbind.scan1perm

Combine data from scan1perm objects

Read phenotype data

Drop all but a specified set of markers

rbind.calc_genoprob

Join genotype probabilities for different individuals

Calculate QTL effects in scan along one chromosome

reduce_map_gaps

Reduce the lengths of gaps in a map

Smooth genetic map

Recode SNPs by major allele

Calculate BLUPs of QTL effects in scan along one chromosome

Installed version of R/qtl2

Simulate genotypes given observed marker data

subset.calc_genoprob

Subsetting genotype probabilities

Subsetting data for a QTL experiment

Convert strain distribution patterns to character strings

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

Single-QTL genome scan at imputed SNPs

Replace individual IDs

subset.sim_geno

Subsetting imputed genotypes

Subsetting Viterbi results

Create table of top snp associations

Calculate most probable sequence of genotypes

plot_genoprobcomp

Plot comparison of two sets of genotype probabilities

print.summary.scan1perm

Print summary of scan1perm permutations

Plot genotype probabilities for one individual on one chromosome.

Subset scan1 output

Unsmooth genetic map

Summary of cross2 object

Print a cross2 object

summary_compare_geno

Basic summary of compare_geno object

Join genotype imputations for different individuals

write_control_file

Write a control file for QTL data

Join Viterbi results for different individuals

summary_scan1perm

Summarize scan1perm results

Get x-axis position for genomic location

Scale kinship matrix

Genome scan with a single-QTL model

Permutation test for genome scan with a single-QTL model

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

Zip a set of data files

Calculate entropy of genotype probability distribution

Calculate genotype frequencies

Calculate conditional genotype probabilities

Collaborative Cross colors

Batch columns by pattern of missing values

Calculate Bayes credible intervals

Split vector into batches

Add thresholds to genome scan plot

Calculate genotyping error LOD scores

basic_summaries

Basic summaries of a cross2 object

cbind.calc_genoprob

Join genotype probabilities for different chromosomes

Calculate estimated heterozygosity from raw SNP genotypes

Calculate kinship matrix

calc_raw_founder_maf

Calculate founder minor allele frequencies from raw SNP genotypes

Calculate heterozygosities

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

Calculate strain distribution pattern from SNP genotypes

Calculate minor allele frequency from raw SNP genotypes