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 (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

1,222

Version

0.30

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 2nd, 2022

Functions in qtl2 (0.30)

Split vector into batches

Add thresholds to genome scan plot

Calculate genotype frequencies

Calculate entropy of genotype probability distribution

Calculate Bayes credible intervals

Batch columns by pattern of missing values

Collaborative Cross colors

basic_summaries

Basic summaries of a cross2 object

Calculate genotyping error LOD scores

Calculate conditional genotype probabilities

Calculate heterozygosities

Calculate strain distribution pattern from SNP genotypes

Calculate estimated heterozygosity from raw SNP genotypes

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

calc_raw_geno_freq

Calculate genotype frequencies from raw SNP genotypes

cbind.calc_genoprob

Join genotype probabilities for different chromosomes

Join genome scan results for different phenotypes.

Join viterbi results for different chromosomes

Calculate minor allele frequency from raw SNP genotypes

Calculate kinship matrix

calc_raw_founder_maf

Calculate founder minor allele frequencies from raw SNP genotypes

Check a cross2 object

Chi-square test on all pairs of columns

Clean scan1 output

Clean genotype probabilities

Join genotype imputations for different chromosomes

cbind.scan1perm

Combine columns from multiple scan1 permutation results

Calculate chromosome lengths

Clean an object

Count numbers of crossovers

Combine matrices by columns, expanding and aligning rows

create_gene_query_func

Create a function to query genes

Compare individuals' genotype data

compare_genoprob

Compare two sets of genotype probabilities

create_variant_query_func

Create a function to query variants

Create snp information table for a cross

Find markers by chromosome position

Find positions of markers

find_ibd_segments

Find IBD segments for a set of strains

Estimate genetic maps

Fit single-QTL model at a single position

Find peaks in a set of LOD curves

Find name of indexed snp

genoprob_to_snpprob

Convert genotype probabilities to SNP probabilities

Find gaps in a genetic map

genoprob_to_alleleprob

Convert genotype probabilities to allele probabilities

Get common set of IDs from objects

Estimate heritability with a linear mixed model

Compare two marker maps

Guess phase of imputed genotypes

Get X chromosome covariates

drop_nullmarkers

Drop markers with no genotype data

Create index of equivalent SNPs

Calculate SNP genotype matrix from strain distribution patterns

Interpolate between maps

Subset a map to positions on a grid

Calculate LOD support intervals

Convert R/qtl cross object to new format

Locate crossovers

Define strata based on rows of a matrix

Drop markers from a cross2 object

Calculate eigen decomposition of kinship matrix

insert_pseudomarkers

Insert pseudomarkers into a marker map

Overall maximum LOD score

Find genotypes with maximum marginal probabilities

plot_compare_geno

Plot of compare_geno object.

plot_genoprobcomp

Plot comparison of two sets of genotype probabilities

Plot genotype probabilities for one individual on one chromosome.

max_compare_geno

Find pair with most similar genotypes

Find position with maximum LOD score

Count missing genotypes

Plot a genome scan

plot strain distribution patterns for SNPs

interp_genoprob

Interpolate genotype probabilities

Plot QTL effects along chromosome

pull_genoprobpos

Pull genotype probabilities for a particular position

Drop all but a specified set of markers

Print a cross2 object

print.summary.scan1perm

Print summary of scan1perm permutations

Plot LOD scores vs QTL peak locations

Plot one individual's genome-wide genotypes

Plot QTL peak locations

Plot phenotype vs genotype

Join genotype imputations for different individuals

pull_genoprobint

Pull genotype probabilities for an interval

Subset genotype probability array to pseudomarkers on a grid

Read a csv file that has numeric columns

Plot SNP associations

predict_snpgeno

Predict SNP genotypes

Read QTL data from files

Read phenotype data

Plot gene locations for a genomic interval

align_scan1_map

Internal functions

qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Genome scan with a single-QTL model

Read a csv file

Join Viterbi results for different individuals

Scale kinship matrix

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

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

Replace individual IDs

Installed version of R/qtl2

rbind.calc_genoprob

Join genotype probabilities for different individuals

Permutation test for genome scan with a single-QTL model

Subsetting Viterbi results

Subset scan1 output

Recode SNPs by major allele

reduce_map_gaps

Reduce the lengths of gaps in a map

Zip a set of data files

Single-QTL genome scan at imputed SNPs

Get x-axis position for genomic location

Convert strain distribution patterns to character strings

subset.calc_genoprob

Subsetting genotype probabilities

Simulate genotypes given observed marker data

Calculate most probable sequence of genotypes

write_control_file

Write a control file for QTL data

Calculate BLUPs of QTL effects in scan along one chromosome

Calculate QTL effects in scan along one chromosome

Join genome scan results for different chromosomes.

rbind.scan1perm

Combine data from scan1perm objects

summary_scan1perm

Summarize scan1perm results

subset.sim_geno

Subsetting imputed genotypes

Create table of top snp associations

Subsetting data for a QTL experiment

Summary of cross2 object

summary_compare_geno

Basic summary of compare_geno object