# A Framework of Functions to Combine, Analize and Interpret CNVs Calling Results

## Documentation for package ‘CNVgears’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

chr_uniform | Uniform chromosome notation
cleaning_filter | Filter CNVs calls based on several parameters
cnmops_to_CNVresults | Convert cn.mops results into 'CNVgears' format
CNVgears | CNVgears: A package to analyze CNVs calling/segmentation results
CNVresults_to_GRanges | CNVresults to GRanges
cnvrs_create | Compute Copy Number Variable Regions (CNVRs)
cnvs_inheritance | Compute CNVs inheritance
cohort_examples | Sample list for the runnable examples. It comes from CNV calling on array data from a subset of the 1000 Genomes project, see vignettes for more details.
genic_load | Annotate genic load
genomic_locus | Rapid genomic locus annotator for CNV calls
hg18_chr_arms | Chromosomal location of the genomic arms for the assembly hg18
hg18_start_end_centromeres | Start, end and centrosome location of each chromosome for the assembly hg18
hg19_chr_arms | Chromosomal location of the genomic arms for the assembly hg19
hg19_start_end_centromeres | Start, end and centrosome location of each chromosome for the assembly hg19
hg38_chr_arms | Chromosomal location of the genomic arms for the assembly hg38
hg38_start_end_centromeres | Start, end and centrosome location of each chromosome for the assembly hg38
immuno_regions | Retrieve genomic regions of consecutive immunoglobulin genes
inter_res_merge | Combine the results from multiple methods in a single object
lrr_trio_plot | Plot markers raw data in a CNV region for a trio
markers_examples | Markers file for the runnable examples It comes from CNV calling on array data from a subset of the 1000 Genomes project, see vignettes for more details.
merge_calls | Merge adjacent CNV with equal Copy Number
penn_22 | Chromosome 22 PennCNV example results for the runnable examples The results of CNV calling using the program PennCNV on array data from a subset of the 1000 Genomes project, see vignettes for more details. Only chromosome 22 was kept in order to keep the object small.
quanti_22 | Chromosome 22 QuantiSNP example results for the runnable examples. The results of CNV calling using the program QuantiSNP on array data from a subset of the 1000 Genomes project, see vignettes for more details. Only chromosome 22 was kept in order to keep the object small.
read_finalreport_raw | Read Illumina array raw data
read_finalreport_snps | Read Illumina array raw data
read_metadt | Read sample file with minimal metadata
read_NGS_intervals | Read genomic intervals
read_NGS_raw | Read raw copyratio/LRR data for NGS intervals
read_results | Read CNVs calling or semgentation results
read_vcf | Convert a VCF file of genomics segments into a 'data.table'
summary.CNVresults | Explore CNV calling results prior filtering
telom_centrom | Generate blacklist for telomeric and centromeric regions