nanotatoR: next generation structural variant annotation and classification

Documentation for package ‘nanotatoR’ version 1.8.0

nanotatoR-package	nanotatoR: Annotation package for Bionano Data
buildrunBNBedFiles	Reads BED files to produce bionano Bed files
clinvar_gene	Extracting genes from clinvar database NCBI.
cohortFrequency	Calculates the internal frequencies of SV in bionano cohorts
compSmapbed	Extracts gene information from bed files
Decipher_extraction	Frequency calculation of variants compared to DGV.
DGV_extraction	Frequency calculation of variants compared to DGV.
gene_extraction	Extracting genes from gene database NCBI.
gene_list_generation	Extracting genes for phenotype/diseases from NCBI.
gtr_gene	Extracting genes from gtr database NCBI.
internalFrequency	Calculates the internal frequencies of SV in internal cohorts
makeMergedSmapData	Merges Bionano SV files to one common SV file
makeMergedSVData	Merges Solo SV files to one common SV file
nanotatoR	nanotatoR: Annotation package for Bionano Data
nanotatoR_main	Annotation of Bionano SV.
nonOverlapGenes	Calculates Genes that are near to the SV region
omim_gene	Extracting genes from OMIM database NCBI.
overlapGenes	Calculates Genes that overlap the SV region
readBNBedFiles	Reads Bionano Bedfiles
readSMap	Reads SMAP files to extract information
run_bionano_filter	Getting the data from annotated smaps to extract SV information based on type of variants.