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qtl2pattern (version 1.2.1)

Pattern Support for 'qtl2' Package

Description

Routines in 'qtl2' to study allele patterns in quantitative trait loci (QTL) mapping over a chromosome. Useful in crosses with more than two alleles to identify how sets of alleles, genetically different strands at the same locus, have different response levels. Plots show profiles over a chromosome. Can handle multiple traits together. See .

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Install

install.packages('qtl2pattern')

Monthly Downloads

197

Version

1.2.1

License

GPL-3

Issues

0

Pull Requests

0

Stars

1

Forks

1

Maintainer

Brian Yandell

Last Published

March 11th, 2023

Functions in qtl2pattern (1.2.1)

read_probs

Read genotype probability object from file
summary.gene_snp

Summary of genes overlapping SNPs
snpprob_collapse

Collapse genoprob according to pattern
sdp_to_pattern

Convert sdp to pattern
gene_exon

Get exons for set of genes
ggplot_merge_feature

Plot of merge_feature object
pattern_diplos

Extract pattern of diplotypes
top_snps_pattern

Top SNPs organized by allele pattern
snpinfo_to_map

Convert SNP info to map
ggplot_scan1pattern

Plot scan pattern usign ggplot2
pattern_label

Turn genotype probabilities into labels
read_fast

Read fast database with possible rownames
summary.feature_snp

Summary of features with SNP information
create_probs_query_func

Create a function to query genotype probabilities
allele1

Allele plot for SNPs, alleles and allele pairs
get.gene.locations

Helper function to set gene locations on plot.
get_feature_snp

Match features with SNPs
genoprob_to_patternprob

Collapse genoprob according to pattern
get_gene_snp

Match genes with SNPs
summary.feature_tbl

Summary of features