An Interface for GenBank/GenPept Flat Files

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Documentation for package ‘biofiles’ version 1.0.0

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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.