Pattern Support for 'qtl2' Package

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Documentation for package ‘qtl2pattern’ version 1.2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

allele1	Allele plot for SNPs, alleles and allele pairs
autoplot.allele1	Allele plot for SNPs, alleles and allele pairs
autoplot.feature_tbl	Summary of features
autoplot.gene_exon	Get exons for set of genes
autoplot.merge_feature	Plot of merge_feature object
autoplot.scan1pattern	Plot scan pattern usign ggplot2
create_probs_query_func	Create a function to query genotype probabilities
gene_exon	Get exons for set of genes
genoprob_to_patternprob	Collapse genoprob according to pattern
get.gene.locations	Helper function to set gene locations on plot.
get_feature_snp	Match features with SNPs
get_gene_snp	Match genes with SNPs
ggplot_allele1	Allele plot for SNPs, alleles and allele pairs
ggplot_feature_tbl	Summary of features
ggplot_gene_exon	Get exons for set of genes
ggplot_merge_feature	Plot of merge_feature object
ggplot_scan1pattern	Plot scan pattern usign ggplot2
merge_feature	Plot of merge_feature object
pattern_diplos	Extract pattern of diplotypes
pattern_haplos	Extract pattern of diplotypes
pattern_label	Turn genotype probabilities into labels
pattern_sdp	Turn genotype probabilities into labels
read_fast	Read fast database with possible rownames
read_probs	Read genotype probability object from file
scan1pattern	Plot scan pattern usign ggplot2
sdp_to_logical	Convert sdp to pattern
sdp_to_pattern	Convert sdp to pattern
snpinfo_to_map	Convert SNP info to map
snpprob_collapse	Collapse genoprob according to pattern
subset.feature_tbl	Summary of features
subset.gene_exon	Get exons for set of genes
subset.top_snps_pattern	Top SNPs organized by allele pattern
summary.feature_snp	Summary of features with SNP information
summary.feature_tbl	Summary of features
summary.gene_exon	Get exons for set of genes
summary.gene_snp	Summary of genes overlapping SNPs
summary.merge_feature	Plot of merge_feature object
summary.scan1pattern	Plot scan pattern usign ggplot2
summary.top_snps_pattern	Top SNPs organized by allele pattern
top_snps_pattern	Top SNPs organized by allele pattern