Man pages for SinomeM/CNVgears
A Framework to Combine, Analize and Interpret CNVs Calling Results
| 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... |
| 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... |
| 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_start_end_centromeres | Start, end and centrosome location of each chromosome for the... |
| hg19_chr_arms | Chromosomal location of the genomic arms for the assembly... |
| hg19_start_end_centromeres | Start, end and centrosome location of each chromosome for the... |
| hg38_chr_arms | Chromosomal location of the genomic arms for the assembly... |
| hg38_start_end_centromeres | Start, end and centrosome location of each chromosome for the... |
| 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... |
| merge_calls | Merge adjacent CNV with equal Copy Number |
| penn_22 | Chromosome 22 PennCNV example results for the runnable... |
| quanti_22 | Chromosome 22 QuantiSNP example results for the runnable... |
| 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 |
