Integrated Copy Number Variation detection

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Documentation for package ‘iCNV’ version 1.20.0

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

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