Man pages for iCNV
Integrated Copy Number Variation detection
| 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 |
