Next generation structural variant annotation and classification


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Documentation for package ‘nanotatoR’ version 1.18.0

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BNDBfrequency Calculates the internal frequencies of BNDB cohorts
buildrunBNBedFiles Reads BED files to produce bionano Bed files
clinvar_gene Extracting genes from clinvar database NCBI.
Decipherfrequency Frequency calculation of variants compared to Decipher.
DGVfrequency Frequency calculation of variants compared to DGV.
extract_clinvar_mod Extract the genes and variants related to a genetic disorder from ClinVar
FamilyInfoPrep Mapping Realtionship to unique nanoIDs
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.
internalFrequencyTrio_Duo Calculates the internal frequencies of SV in internal cohorts, for SVMerge
internalFrequency_solo Calculates the internal frequencies of SV in internal cohorts, for SE
makeInternalBNDatabase Merges Solo SV files to one common SV file
mergingSMAP_SE Merging DLE labelled smaps
mergingSMAP_SVMerge Merging dual labelled smaps
merging_SE_SVMerge Merging Dual and DLE, and adding nanotatoR relation ID
nanotatoR nanotatoR: Annotation package for Bionano Data
nanotatoR_Duo_SVmerge Annotation and visualisation of Bionano SV, of SVMerge Duo samples.
nanotatoR_main_Duo_SE Annotation and visualisation of Bionano SV, of Single enzyme Duo samples.
nanotatoR_main_Solo_SE Annotation and visualisation of Bionano SV, of DLE Solo samples.
nanotatoR_main_Solo_SVmerge Annotation and visualisation of Bionano SV, of Solo SVMerge samples.
nanotatoR_main_Trio_SE Annotation and visualisation of Bionano SV, of DLE Trio samples.
nanotatoR_SVmerge_Trio Annotation and visualisation of Bionano SV, of DLE Trio samples.
nonOverlapGenes Calculates Genes that are near to the SV region
nonOverlappingDNGenes Extracting terms for genes that overlap SVs
nonOverlappingUPGenes Extracting terms for genes that overlap SVs
nonOverlapRNAseq Extract Read counts for genes that are near SVs.
nonOverlapRNAseq_solo Annotating the Non-Overlapping genes with RNAseq expression
omim_gene Extracting genes from OMIM database NCBI.
overlapGenes Calculates Genes that overlap the SV region
overlapnearestgeneSearch Extracts gene information from bed files
overlappingGenes Extracting terms for genes that overlap SVs
OverlapRNAseq Extract Read counts for genes that overlap SVs.
OverlapRNAseq_solo Annotating the Overlapping genes with RNAseq expression
phenoextractHPO_mod Extract the genes related to a disease or disease alias from HPO database.
readBNBedFiles Reads Bionano Bedfiles
reading_GTR Reading and parsing gtr database.
reading_mim2gene Reading and parsing OMIM database.
readSMap Reads SMAP files to extract information from SVMerge
readSMap_DLE Reads DLE SMAP files to extract information
RNAseqcombine Combining the RNAseq reads of family members in a single file.
RNAseqcombine_solo Combining the RNAseq reads of family members in a single file.
run_bionano_filter_SE_duo Getting the data from annotated smaps to extract SV information based on type of variants.
run_bionano_filter_SE_solo Getting the data from annotated smaps to extract SV information based on type of variants.
run_bionano_filter_SE_Trio Getting the data from annotated smaps to extract SV information based on type of variants.
run_bionano_filter_SVMerge_duo Getting the data from annotated smaps to extract SV information based on type of variants.
run_bionano_filter_SVMerge_solo Getting the data from annotated smaps to extract SV information based on type of variants.
run_bionano_filter_SVMerge_Trio Getting the data from annotated smaps to extract SV information based on type of variants.
SVexpression_duo_trio Extract Read counts for genes that are near or overalapping SVs.
SVexpression_solo Annotating the Overlapping and Non-Overlapping genes with RNAseq expression