# An Interface for GenBank/GenPept Flat Files

## Documentation for package ‘biofiles’ version 1.0.0

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

## Help Pages

A B D E F G H I J K L N P Q R S T U W misc

biofiles-package | _biofiles_ is an R package for interfacing with GenBank or Embl flat file records.

## -- A --

as.gbLocation | Create a 'gbLocation'.

## -- B --

biofiles | _biofiles_ is an R package for interfacing with GenBank or Embl flat file records.

## -- D --

dbxref | Access the 'db_xref's of GenBank features
dbxref-method | Access the 'db_xref's of GenBank features
downstream | Find flanking features.

## -- E --

end | Get or set the end position of genomic features
end-method | Get or set the end position of genomic features
end<- | Get or set the end position of genomic features
end<--method | Get or set the end position of genomic features

## -- F --

featureTable | Tabulate Genbank features
featureTable-method | Tabulate Genbank features
filter | Return a subset of features or annotations from a GenBank Record
filter-method | Return a subset of features or annotations from a GenBank Record
flanking | Find flanking features.
ft | Get the feature table from a GenBank record.
ft-method | Get the feature table from a GenBank record.
fuzzy | Has a feature fuzzy locations?
fuzzy-method | Has a feature fuzzy locations?

## -- G --

gbFeature-class | Class '"gbFeature"'
gbFeatureTable-class | Class '"gbFeatureTable"'
gbRecord | Read a GenBank/GenPept or Embl format file.
gbRecord-class | Class '"gbRecord"'
gbRecordList | Class '"gbRecordList"'
gbRecordList-class | Class '"gbRecordList"'
geneID | Return the _gene_ qualifiers from GenBank features.
getAccession | Access the various fields of a GenBank record.
getAccession-method | Access the various fields of a GenBank record.
getComment | Access the various fields of a GenBank record.
getComment-method | Access the various fields of a GenBank record.
getDate | Access the various fields of a GenBank record.
getDate-method | Access the various fields of a GenBank record.
getDBLink | Access the various fields of a GenBank record.
getDBLink-method | Access the various fields of a GenBank record.
getDBSource | Access the various fields of a GenBank record.
getDBSource-method | Access the various fields of a GenBank record.
getDefinition | Access the various fields of a GenBank record.
getDefinition-method | Access the various fields of a GenBank record.
getDivision | Access the various fields of a GenBank record.
getDivision-method | Access the various fields of a GenBank record.
getFeatures | Get the feature table from a GenBank record.
getFeatures-method | Get the feature table from a GenBank record.
getGeneID | Access the various fields of a GenBank record.
getGeneID-method | Access the various fields of a GenBank record.
getHeader | Extract the header from a '"gbRecord"' object.
getHeader-method | Extract the header from a '"gbRecord"' object.
getKeywords | Access the various fields of a GenBank record.
getKeywords-method | Access the various fields of a GenBank record.
getLength | Access the various fields of a GenBank record.
getLength-method | Access the various fields of a GenBank record.
getLocus | Access the various fields of a GenBank record.
getLocus-method | Access the various fields of a GenBank record.
getMoltype | Access the various fields of a GenBank record.
getMoltype-method | Access the various fields of a GenBank record.
getOrganism | Access the various fields of a GenBank record.
getOrganism-method | Access the various fields of a GenBank record.
getReference | Access the various fields of a GenBank record.
getReference-method | Access the various fields of a GenBank record.
getSequence | Get the sequence from a GenBank record.
getSequence-method | Get the sequence from a GenBank record.
getSource | Access the various fields of a GenBank record.
getSource-method | Access the various fields of a GenBank record.
getTaxonomy | Access the various fields of a GenBank record.
getTaxonomy-method | Access the various fields of a GenBank record.
getTopology | Access the various fields of a GenBank record.
getTopology-method | Access the various fields of a GenBank record.
getVersion | Access the various fields of a GenBank record.
getVersion-method | Access the various fields of a GenBank record.

## -- H --

hasKey | Has a feature a specific key?
hasKey-method | Has a feature a specific key?
hasQualif | Has a feature a specific qualifier?
hasQualif-method | Has a feature a specific qualifier?
header | Extract the header from a '"gbRecord"' object.
header-method | Extract the header from a '"gbRecord"' object.

## -- I --

index | Access the indices of GenBank features
index-method | Access the indices of GenBank features

## -- J --

joint_range | Get the span of genomic features.
joint_range-method | Get the span of genomic features.

## -- K --

key | Get/set keys of GenBank features
key-method | Get/set keys of GenBank features
key<- | Get/set keys of GenBank features
key<--method | Get/set keys of GenBank features

## -- L --

length-method | Get the number of gbFeatures.
loadRecord | Save and load 'gbRecord' objects.
location | Access genomic locations of GenBank features
location-method | Access genomic locations of GenBank features
locusTag | Return the _locus_tag_ qualifiers from GenBank features.

## -- N --

new_gbRecord | Class '"gbRecord"'
note | Return the _note_ qualifiers from GenBank features.

## -- P --

product | Return the _product_ qualifiers from GenBank features.
proteinID | Return the _protein_id_ qualifiers from GenBank features.

## -- Q --

qualif | Get/set qualifiers of GenBank features
qualif-method | Get/set qualifiers of GenBank features
qualif<- | Get/set qualifiers of GenBank features
qualif<--method | Get/set qualifiers of GenBank features
qualifList | List the names of Genbank qualifiers.
qualifList-method | List the names of Genbank qualifiers.
qualifTable | Tabulate Genbank qualifiers
qualifTable-method | Tabulate Genbank qualifiers

## -- R --

ranges | Extract features as '"GRanges"' objects.
ranges-method | Extract features as '"GRanges"' objects.
revcomp | Reverse-complement features in a GenBank record
revcomp-method | Reverse-complement features in a GenBank record

## -- S --

saveRecord | Save and load 'gbRecord' objects.
saveRecord-method | Save and load 'gbRecord' objects.
select | Return a subset of features or annotations from a GenBank Record
select-method | Return a subset of features or annotations from a GenBank Record
shift | Shift the location of features in a GenBank record
shift-method | Shift the location of features in a GenBank record
span | Get the span of genomic features.
span-method | Get the span of genomic features.
start | Get or set the start position of genomic features
start-method | Get or set the start position of genomic features
start<- | Get or set the start position of genomic features
start<--method | Get or set the start position of genomic features
strand | Get or set the strand information of genomic features
strand-method | Get or set the strand information of genomic features
strand<- | Get or set the strand information of genomic features
strand<--method | Get or set the strand information of genomic features
summary | Summarise a GenBank record.
summary-method | Summarise a GenBank record.

## -- T --

translation | Return the _translation_s from GenBank features.

## -- U --

uniqueQualifs | Quickly list all qualifier names.
upstream | Find flanking features.

## -- W --

write.FeatureTable | Write GenBank records or features to file in Feature Table format
write.FeatureTable-method | Write GenBank records or features to file in Feature Table format
write.GenBank | Write GenBank records or features to file in GenBank format
write.GenBank-method | Write GenBank records or features to file in GenBank format

## -- misc --

$-method | Method extensions to extraction operator for gbRecord objects.
[-method | Method extensions to extraction operator for gbRecord objects.
[[-method | Method extensions to extraction operator for gbRecord objects.