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 package, qtl2convert, for converting data among the R/qtl2, DOQTL, and R/qtl formats.

Installation

Install R/qtl2 from CRAN:

install.packages("qtl2")

Vignettes

user guide
input file formats (see also the sample data files and the qtl2data repository)
preparing DO mouse data for R/qtl2
differences between R/qtl and R/qtl2
developer guide
HMM benchmarks

Citation

To cite R/qtl2 in publications, use:

Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2018) 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

678

Version

0.24

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/rqtl/qtl2

Homepage

https://kbroman.org/qtl2/

Maintainer

Karl Broman

Last Published

December 18th, 2020

Functions in qtl2 (0.24)

Collaborative Cross colors

Calculate genotype frequencies

Batch columns by pattern of missing values

Add thresholds to genome scan plot

Calculate conditional genotype probabilities

Calculate genotyping error LOD scores

Calculate entropy of genotype probability distribution

basic_summaries

Basic summaries of a cross2 object

Split vector into batches

Calculate Bayes credible intervals

Calculate kinship matrix

calc_raw_founder_maf

Calculate founder minor allele frequencies from raw SNP genotypes

Join viterbi results for different chromosomes

Calculate strain distribution pattern from SNP genotypes

Calculate minor allele frequency from raw SNP genotypes

cbind.scan1perm

Combine columns from multiple scan1 permutation results

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

Join genotype imputations for different chromosomes

Calculate heterozygosities

Combine matrices by columns, expanding and aligning rows

Chi-square test on all pairs of columns

Count numbers of crossovers

Check a cross2 object

create_gene_query_func

Create a function to query genes

Compare individuals' genotype data

compare_genoprob

Compare two sets of genotype probabilities

Join genome scan results for different phenotypes.

cbind.calc_genoprob

Join genotype probabilities for different chromosomes

Clean genotype probabilities

Clean scan1 output

Create snp information table for a cross

drop_nullmarkers

Drop markers with no genotype data

Estimate heritability with a linear mixed model

Find gaps in a genetic map

Find name of indexed snp

Calculate eigen decomposition of kinship matrix

create_variant_query_func

Create a function to query variants

Calculate estimated heterozygosity from raw SNP genotypes

calc_raw_geno_freq

Calculate genotype frequencies from raw SNP genotypes

Find markers by chromosome position

Find positions of markers

Drop markers from a cross2 object

Overall maximum LOD score

insert_pseudomarkers

Insert pseudomarkers into a marker map

interp_genoprob

Interpolate genotype probabilities

Interpolate between maps

Calculate SNP genotype matrix from strain distribution patterns

Calculate chromosome lengths

Guess phase of imputed genotypes

Find peaks in a set of LOD curves

Create index of equivalent SNPs

Find genotypes with maximum marginal probabilities

Get X chromosome covariates

Calculate LOD support intervals

Locate crossovers

Get common set of IDs from objects

Recode SNPs by major allele

Read phenotype data

Fit single-QTL model at a single position

Define strata based on rows of a matrix

Subset a map to positions on a grid

max_compare_geno

Find pair with most similar genotypes

Find position with maximum LOD score

Plot QTL peak locations

Plot phenotype vs genotype

predict_snpgeno

Predict SNP genotypes

Plot SNP associations

Plot a genome scan

Replace individual IDs

pull_genoprobint

Pull genotype probabilities for an interval

Print a cross2 object

Clean an object

Compare two marker maps

Scale kinship matrix

summary_compare_geno

Basic summary of compare_geno object

Permutation test for genome scan with a single-QTL model

Convert strain distribution patterns to character strings

Single-QTL genome scan at imputed SNPs

Simulate genotypes given observed marker data

summary_scan1perm

Summarize scan1perm results

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

Calculate QTL effects in scan along one chromosome

rbind.scan1perm

Combine data from scan1perm objects

pull_genoprobpos

Pull genotype probabilities for a particular position

Join genotype imputations for different individuals

subset.sim_geno

Subsetting imputed genotypes

Plot genotype probabilities for one individual on one chromosome.

Estimate genetic maps

Convert R/qtl cross object to new format

plot_compare_geno

Plot of compare_geno object.

plot_genoprobcomp

Plot comparison of two sets of genotype probabilities

qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

genoprob_to_alleleprob

Convert genotype probabilities to allele probabilities

Count missing genotypes

find_ibd_segments

Find IBD segments for a set of strains

Plot QTL effects along chromosome

genoprob_to_snpprob

Convert genotype probabilities to SNP probabilities

Plot LOD scores vs QTL peak locations

Plot gene locations for a genomic interval

rbind.calc_genoprob

Join genotype probabilities for different individuals

Installed version of R/qtl2

Join genome scan results for different chromosomes.

Genome scan with a single-QTL model

Subsetting Viterbi results

Calculate BLUPs of QTL effects in scan along one chromosome

Subset genotype probability array to pseudomarkers on a grid

Read a csv file

print.summary.scan1perm

Print summary of scan1perm permutations

Create table of top snp associations

Calculate most probable sequence of genotypes

Subset scan1 output

reduce_map_gaps

Reduce the lengths of gaps in a map

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

Read a csv file that has numeric columns

Plot one individual's genome-wide genotypes

align_scan1_map

Internal functions

Drop all but a specified set of markers

Join Viterbi results for different individuals

subset.calc_genoprob

Subsetting genotype probabilities

Read QTL data from files

Summary of cross2 object

Zip a set of data files

write_control_file

Write a control file for QTL data

Get x-axis position for genomic location

Subsetting data for a QTL experiment