# Pattern Support for 'qtl2' Package

## 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