R for genes and sequences analysis

Documentation for package ‘GeneR’ version 2.24.0

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-- A --

and	Intersection of segments
and.default	Intersection of segments
and.globalSeg	Intersection of global segments
and.segSet	Intersection of segments
appendSeq	Appends two sequences
as.data.frame.segSet	Segments Set manipulation
as.globalSeg	GlobalSeg manipulation
as.matrix.globalSeg	GlobalSeg manipulation
as.matrix.segSet	Segments Set manipulation
as.segSet	Segments Set manipulation
assemble	Concatenates parts of a sequence
AtoR	Conversion of addresses
AtoT	Conversion of addresses

-- B --

bankDensityProfile	Computes density profile(s) of a bank of fasta sequences
bankSummary	Computes informations on all a bank file

-- C --

compoSeq	Composition in mono, di or trinucleotides of a sequence
concat	Concatenation of two sequences

-- D --

deleteCR	Delete carriage return in file
densityProfile	Density profiles
dnaToRna	DNA <-> RNA sequence rewriting

-- E --

Exact matches of an oligomer

-- F --

fastaDescription	Description field reading of a fasta sequence
freeAllSeq	Low level functions on buffer manipulation
freeSeq	Low level functions on buffer manipulation

-- G --

GCcontent	compute the strand assymetries from one sequence fragment
GeneR	Overview of GeneR package
getAccn	Reading of a GeneR global variable
getBegSeq	Reading of a GeneR global variable
getEndSeq	Reading of a GeneR global variable
getOrfs	Gets ORFs from a sequence
getParam	Reading of all the GeneR global variables
getSeq	Sequence fragments extraction
getSeqSize	Reading of a GeneR global variable
getStrand	Reading of a GeneR global variable
globals	Globals variables on Gene sequences
globalSeg	Class manipulating segments

-- I --

indexEmbl	Index file creation for a sequences bank
indexFasta	Index file creation for a sequences bank
indexGbk	Index file creation for a sequences bank
insertSeq	Sequence insertion

-- L --

Length	Size.globalSeg
Length.default	Size.globalSeg
Length.globalSeg	Size.globalSeg
lowerSeq	Convert upper/lower-case characters in sequence fragments

-- M --

makeIndex	Index file creation for a bank file (internal function)
mask	Mask regions on a sequence
Match	Value Matching
Max	Size.globalSeg
Max.default	Size.globalSeg
Max.globalSeg	Size.globalSeg
maxOrf	Gets ORFs from a sequence
Min	Size.globalSeg
Min.default	Size.globalSeg
Min.globalSeg	Size.globalSeg

-- N --

not	Substraction of segments sets
not.default	Substraction of segments sets
not.globalSeg	Substraction of globals segments
not.segSet	Substraction of segments sets
nSeq	Low level functions on buffer manipulation

-- O --

-- P --

placeString	Sequence loading in a GeneR sequence buffer.
plot.globalSeg	Plot an object of class globalSeg
plot.profile	Density profiles
plot.segSet	Segments Set manipulation
posMaskedSeq	Position of masked fragments
posMaskedSeqFile	Position of masked fragments

-- R --

randomSeq	Create random sequence
range.globalSeg	GlobalSeg manipulation
readEmbl	Sequence extraction from a bank
readEmblDescript	Read features from an Embl bank file
readEmblLocation	Get annotations of a GeneBank or an EMBL sequence
readFasta	Sequence extraction from a bank
readGbk	Sequence extraction from a bank
readGbkLocation	Get annotations of a GeneBank or an EMBL sequence
readSeq	Sequence extraction from a bank
relist	Group segments into global segments
relistage	Group segments into global segments
revComp	Performs the reverse of a sequence
rnaToDna	DNA <-> RNA sequence rewriting
RtoA	Conversion of addresses
RtoT	Conversion of addresses

-- S --

seqNcbi	Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs
seqSkew	compute the strand assymetries from one sequence fragment
seqSrs	Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs
seqUrl	Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs
setAccn	Set globals variables of a sequence
setBegSeq	Set globals variables of a sequence
setParam	Set global variables associated to a sequence
setSeqSize	Set globals variables of a sequence
setStrand	Set globals variables of a sequence
showTable	Translation from DNA trinucleotides to proteine
shuffleSeq	Create random sequence
size	Size.globalSeg
size.default	Size.globalSeg
size.globalSeg	Size.globalSeg
sizeSeq	Size of a sequence in a buffer
sizeSeqEmbl	Size of a sequence from a fasta/embl/gbk file
sizeSeqFasta	Size of a sequence from a fasta/embl/gbk file
sizeSeqGbk	Size of a sequence from a fasta/embl/gbk file
sliceSegment	delineate sub-segments of equal size at both sides of an origin in a segment
strComp	Performs the reverse of a sequence
strCompoSeq	Composition in mono, di or trinucleotides of a sequence
strReadEmbl	Sequence extraction from a bank
strReadFasta	Sequence extraction from a bank
strReadGbk	Sequence extraction from a bank
strTranslate	Translation from DNA trinucleotides to proteine
strWriteFasta	Write sequences into fasta file format

-- T --

translate	Translation from DNA trinucleotides to proteine
TtoA	Conversion of addresses
TtoR	Conversion of addresses

-- U --

unionSeg	Union of 2 segments sets
upperSeq	Convert upper/lower-case characters in sequence fragments

-- W --

writeEmbl	Write to Embl file
writeEmblComment	Write to Embl file
writeEmblLine	Write to Embl file
writeEmblSeq	Write to Embl file
writeFasta	Write sequences into fasta file format

-- X --

-- misc --

&.globalSeg	Intersection of global segments
-.globalSeg	Substraction of globals segments
-.segSet	Substraction of segments sets
.seqSize	Size of a sequence in a buffer
\|.globalSeg	Union of global segments