Candidate Gene Miner


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Documentation for package ‘cageminer’ version 1.4.0

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