CNVgears                CNVgears: A package to analyze CNVs
                        calling/segmentation results
CNVresults_to_GRanges   CNVresults to GRanges
chr_uniform             Uniform chromosome notation
cleaning_filter         Filter CNVs calls based on several parameters
cnmops_to_CNVresults    Convert cn.mops results into 'CNVgears' format
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_NGS_intervals      Read genomic intervals
read_NGS_raw            Read raw copyratio/LRR data for NGS intervals
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_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
