R for genes and sequences analysis


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Documentation for package ‘GeneR’ version 2.24.0

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A B C D E F G I L M N O P R S T U W X misc

-- 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 --

exactWord 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 --

or Union of 2 segments sets
or.default Union of 2 segments sets
or.globalSeg Union of global segments
or.segSet Union of 2 segments sets

-- 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 --

Xor Xor for segments sets
Xor.default Xor for segments sets
Xor.globalSeg Xor for global segments
Xor.segSet Xor for segments sets
xorRecouvr Xor for segments sets

-- 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