qtl2 package - RDocumentation

Learn R Programming

⚠️There's a newer version (0.36) of this package.Take me there.

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.

Copy Link

Version

Install

install.packages('qtl2')

Monthly Downloads

625

Version

0.32

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/rqtl/qtl2

Homepage

https://kbroman.org/qtl2/

Maintainer

Karl Broman

Last Published

April 22nd, 2023

Functions in qtl2 (0.32)

Calculate Bayes credible intervals

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.

Calculate heterozygosities

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

Clean an object

Calculate chromosome lengths

Calculate estimated heterozygosity from raw SNP genotypes

Clean genotype probabilities

Batch columns by pattern of missing values

Calculate kinship matrix

Clean scan1 output

basic_summaries

Basic summaries of a cross2 object

Calculate minor allele frequency from raw SNP genotypes

Check a cross2 object

Calculate strain distribution pattern from SNP genotypes

Chi-square test on all pairs of columns

calc_raw_founder_maf

Calculate founder minor allele frequencies from raw SNP genotypes

cbind.scan1perm

Combine columns from multiple scan1 permutation results

create_gene_query_func

Create a function to query genes

Count numbers of crossovers

Find peaks in a set of LOD curves

Calculate eigen decomposition of kinship matrix

Join viterbi results for different chromosomes

Combine matrices by columns, expanding and aligning rows

Create snp information table for a cross

Drop markers from a cross2 object

create_variant_query_func

Create a function to query variants

Find markers by chromosome position

Find positions of markers

Find name of indexed snp

insert_pseudomarkers

Insert pseudomarkers into a marker map

genoprob_to_alleleprob

Convert genotype probabilities to allele probabilities

genoprob_to_snpprob

Convert genotype probabilities to SNP probabilities

Fit single-QTL model at a single position

interp_genoprob

Interpolate genotype probabilities

Find gaps in a genetic map

Compare individuals' genotype data

Count missing genotypes

max_compare_geno

Find pair with most similar genotypes

Find position with maximum LOD score

Join genotype imputations for different chromosomes

Compare two marker maps

Convert R/qtl cross object to new format

Plot QTL peak locations

drop_nullmarkers

Drop markers with no genotype data

Get common set of IDs from objects

Estimate heritability with a linear mixed model

Plot phenotype vs genotype

align_scan1_map

Internal functions

compare_genoprob

Compare two sets of genotype probabilities

qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Plot QTL effects along chromosome

rbind.calc_genoprob

Join genotype probabilities for different individuals

Installed version of R/qtl2

Subset genotype probability array to pseudomarkers on a grid

Plot a genome scan

find_ibd_segments

Find IBD segments for a set of strains

Interpolate between maps

Estimate genetic maps

plot strain distribution patterns for SNPs

pull_genoprobint

Pull genotype probabilities for an interval

Guess phase of imputed genotypes

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

Join genome scan results for different chromosomes.

Get X chromosome covariates

Permutation test for genome scan with a single-QTL model

Simulate genotypes given observed marker data

Overall maximum LOD score

Find genotypes with maximum marginal probabilities

Calculate LOD support intervals

Plot genotype probabilities for one individual on one chromosome.

plot_genoprobcomp

Plot comparison of two sets of genotype probabilities

Locate crossovers

Create index of equivalent SNPs

Smooth genetic map

rbind.scan1perm

Combine data from scan1perm objects

pull_genoprobpos

Pull genotype probabilities for a particular position

Calculate SNP genotype matrix from strain distribution patterns

Calculate BLUPs of QTL effects in scan along one chromosome

plot_compare_geno

Plot of compare_geno object.

Calculate QTL effects in scan along one chromosome

Subset a map to positions on a grid

Define strata based on rows of a matrix

Plot one individual's genome-wide genotypes

Print a cross2 object

Plot gene locations for a genomic interval

Plot LOD scores vs QTL peak locations

Calculate most probable sequence of genotypes

Subsetting Viterbi results

subset.sim_geno

Subsetting imputed genotypes

write_control_file

Write a control file for QTL data

Drop all but a specified set of markers

print.summary.scan1perm

Print summary of scan1perm permutations

Join Viterbi results for different individuals

Join genotype imputations for different individuals

Plot SNP associations

Read a csv file

Read QTL data from files

Read a csv file that has numeric columns

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

Replace individual IDs

predict_snpgeno

Predict SNP genotypes

Read phenotype data

Recode SNPs by major allele

Subset scan1 output

Genome scan with a single-QTL model

Scale kinship matrix

Summary of cross2 object

Convert strain distribution patterns to character strings

Single-QTL genome scan at imputed SNPs

Get x-axis position for genomic location

subset.calc_genoprob

Subsetting genotype probabilities

reduce_map_gaps

Reduce the lengths of gaps in a map

Subsetting data for a QTL experiment

Zip a set of data files

Create table of top snp associations

Unsmooth genetic map

summary_compare_geno

Basic summary of compare_geno object

summary_scan1perm

Summarize scan1perm results

Calculate entropy of genotype probability distribution

Calculate genotype frequencies

Add thresholds to genome scan plot

Split vector into batches

Collaborative Cross colors

Calculate conditional genotype probabilities

Calculate genotyping error LOD scores