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

625

Version

0.36

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 13th, 2024

Functions in qtl2 (0.36)

Calculate kinship matrix

Join genome scan results for different phenotypes.

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

calc_raw_founder_maf

Calculate founder minor allele frequencies from raw SNP genotypes

calc_raw_geno_freq

Calculate genotype frequencies from raw SNP genotypes

Calculate minor allele frequency from raw SNP genotypes

Calculate estimated heterozygosity from raw SNP genotypes

Clean genotype probabilities

cbind.scan1perm

Combine columns from multiple scan1 permutation results

Join genotype imputations for different chromosomes

Combine matrices by columns, expanding and aligning rows

Join viterbi results for different chromosomes

Clean an object

Calculate chromosome lengths

Create snp information table for a cross

Clean scan1 output

create_variant_query_func

Create a function to query variants

Drop markers from a cross2 object

Calculate eigen decomposition of kinship matrix

Count numbers of crossovers

create_gene_query_func

Create a function to query genes

Convert R/qtl cross object to new format

Compare two marker maps

compare_genoprob

Compare two sets of genotype probabilities

Compare individuals' genotype data

Find gaps in a genetic map

Check a cross2 object

find_ibd_segments

Find IBD segments for a set of strains

Chi-square test on all pairs of columns

Find name of indexed snp

Find positions of markers

Find peaks in a set of LOD curves

Create index of equivalent SNPs

drop_nullmarkers

Drop markers with no genotype data

Estimate heritability with a linear mixed model

Find markers by chromosome position

Read a csv file

Fit single-QTL model at a single position

insert_pseudomarkers

Insert pseudomarkers into a marker map

find_dup_markers

Find markers with identical genotype data

Interpolate between maps

interp_genoprob

Interpolate genotype probabilities

Find position with maximum LOD score

Calculate SNP genotype matrix from strain distribution patterns

genoprob_to_snpprob

Convert genotype probabilities to SNP probabilities

Get common set of IDs from objects

Overall maximum LOD score

Estimate genetic maps

Locate crossovers

Define strata based on rows of a matrix

fread_csv_numer

Read a csv file that has numeric columns

max_compare_geno

Find pair with most similar genotypes

genoprob_to_alleleprob

Convert genotype probabilities to allele probabilities

plot_genoprobcomp

Plot comparison of two sets of genotype probabilities

Calculate LOD support intervals

Get X chromosome covariates

Plot QTL effects along chromosome

Find genotypes with maximum marginal probabilities

pull_genoprobint

Pull genotype probabilities for an interval

Guess phase of imputed genotypes

Subset a map to positions on a grid

plot_compare_geno

Plot of compare_geno object.

Count missing genotypes

pull_genoprobpos

Pull genotype probabilities for a particular position

Plot one individual's genome-wide genotypes

Plot QTL peak locations

Plot phenotype vs genotype

Plot a genome scan

Plot gene locations for a genomic interval

Plot genotype probabilities for one individual on one chromosome.

predict_snpgeno

Predict SNP genotypes

Join Viterbi results for different individuals

Read QTL data from files

Plot LOD scores vs QTL peak locations

rbind.calc_genoprob

Join genotype probabilities for different individuals

Join genome scan results for different chromosomes.

Print a cross2 object

Join genotype imputations for different individuals

Read phenotype data

rbind.scan1perm

Combine data from scan1perm objects

Plot SNP associations

print.summary.scan1perm

Print summary of scan1perm permutations

Calculate QTL effects in scan along one chromosome

plot strain distribution patterns for SNPs

Recode SNPs by major allele

Drop all but a specified set of markers

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

Genome scan with a single-QTL model

Installed version of R/qtl2

Replace individual IDs

qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

align_scan1_map

Internal functions

Subset genotype probability array to pseudomarkers on a grid

Calculate BLUPs of QTL effects in scan along one chromosome

Scale kinship matrix

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

reduce_map_gaps

Reduce the lengths of gaps in a map

Convert strain distribution patterns to character strings

Subsetting data for a QTL experiment

Single-QTL genome scan at imputed SNPs

Permutation test for genome scan with a single-QTL model

subset.sim_geno

Subsetting imputed genotypes

subset.calc_genoprob

Subsetting genotype probabilities

Smooth genetic map

Subsetting Viterbi results

Subset scan1 output

Simulate genotypes given observed marker data

Unsmooth genetic map

summary_scan1perm

Summarize scan1perm results

Create table of top snp associations

Calculate most probable sequence of genotypes

Get x-axis position for genomic location

Summary of cross2 object

write_control_file

Write a control file for QTL data

summary_compare_geno

Basic summary of compare_geno object

Zip a set of data files

Calculate entropy of genotype probability distribution

basic_summaries

Basic summaries of a cross2 object

Batch columns by pattern of missing values

Calculate genotyping error LOD scores

Calculate conditional genotype probabilities

Calculate genotype frequencies

Add thresholds to genome scan plot

Collaborative Cross colors

Split vector into batches

Calculate Bayes credible intervals