# Integrated Copy Number Variation detection

## Documentation for package ‘iCNV’ version 1.31.0

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

## Help Pages

bambaf_from_vcf | Get BAM baf information from vcf
bed_generator | Generate BED file for WGS dataset.
chr | chromosome of the example
filenm | Name of the file
get_array_input | Get array information from given format
iCNV_detection | CNV detection
icnv_output_to_gb | Convert icnv.output to input for Genome Browser.
icnv_res0 | Example iCNV calling results.
ngs_baf | BAF list from NGS
ngs_baf.chr | BAF chromosome from NGS
ngs_baf.id | BAF variants id from NGS
ngs_baf.nm | BAF variants sample name from NGS
ngs_baf.pos | BAF position list from NGS
ngs_plr | Normalized Poisson likelihood ratio list from NGS
ngs_plr.pos | Exon location list from NGS
normObj | Demo data pre-stored for normObj.
output_list | Generate ouput list.
plotHMMscore | Plot CNV inference score.
plotindi | Individual sample plot
plot_intensity | plot out the NGS plr or array lrr.
projname | name of project
qcObj | Demo data pre-stored for qcObj.
sampname | CODEX sample name
sampname_qc | QCed sample name
snp_baf | BAF list from Array
snp_baf.pos | BAF position list from Array
snp_lrr | Normalized log R ratio list from Array
snp_lrr.pos | SNP position list from Array