# Candidate Gene Miner

## Documentation for package ‘cageminer’ version 1.19.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

chr_length | Pepper chromosome lengths
gcn | Simulation of the output list from BioNERO::exp2gcn() with pepper data
gene_ranges | Genomic coordinates of pepper genes
guides | Guide genes associated with defense and resistance to oomycetes
hubs | Example hub genes for the network stored in the gcn object
mine2 | Example output from mine_step2()
mined_candidates | Example output from mined_candidates()
mine_candidates | Mine high-confidence candidate genes in a single step
mine_step1 | Step 1: Get all putative candidate genes for a given sliding window
mine_step2 | Step 2: Get candidates in modules enriched in guide genes
mine_step3 | Step 3: Select candidates based on gene significance
pepper_se | Gene expression data from Kim et al., 2018.
plot_snp_circos | Circos plot of SNP distribution across chromosomes
plot_snp_distribution | Plot a barplot of SNP distribution across chromosomes
score_genes | Score candidate genes and select the top n genes
simulate_windows | Simulate number of genes for each sliding window
snp_pos | Capsicum annuum SNPs associated with resistance to Phytophthora root rot.
tfs | Pepper transcription factors