Globals Variables {GeneR}R Documentation

Globals variables on Gene sequences

Description

There are two ways to store sequences in GeneR:

Details

When GeneR load a subset of a larger sequence stored in a bank file, it will store the following informations in the C adapted class (buffers, by default 100 buffers than can be extended if necessary):

For specific purposes as renaming a sequence, all these variables can be viewed and carefully changed at any time (here functions getAccn and setAccn).

Several sequences can be stored simultaneously and called by their buffer number.

Strand is another global variable which can be set and viewed (functions getStrand and setStrand). It is used as input parameter in many functions to analyze complementary strand. It was designed to avoid doing explicitly the complement of the loaded strand then to store it in a buffer with, as consequence, loss of the informations linked to the master sequence.

We have defined 3 types of addresses on a subsequence extracted from a master sequence:

Let's show an example, if we read sequence from 11 to 20 from a gene of size 40:

  Strand 0  (Forward strand)
  1         11       20                  40  Absolute (A) 
  1         11       20                  40  Real (R) 
            1        10                      Relative (T)
  xxxxxxxxxxATGTGTCGTAxxxxxxxxxxxxxxxxxxxx
            10       1                       Relative (T)
  40        30       21                  1   Real (R)
  1         11       20                  40  Absolute (A)
  Strand 1  (Reverse strand)

  

Obviously, when an entire sequence is stored, real and relative addresses will be the same.

Although all functions using positions need and return absolute addresses, 6 functions allow to convert R, A, T into any other type (functions RtoA, RtoT, AtoR, AtoT, TtoR, TtoA).

A global variable strand is used to convert positions (see setStrand getStrand).

See Also

AtoT, AtoR, RtoA, RtoT, TtoA, TtoR, setStrand, getStrand, getParam, setParam, getAccn, setAccn

Examples


## Make a dummy sequence
s <- "xxxxxxxxxxATGTGTCGTAxxxxxxxxxxxxxxxxxxxx"
placeString(s)
writeFasta(file="toto.fa")

indexFasta("toto.fa")
readFasta("toto.fa",from=11,to=20)

getParam()
## $begin 
## [1] 11
## $size
## [1] 40
## $strand
## [1] 0
## [...]

## With strand = 0 
TtoA(c(1,10))
##[1] 10 19

TtoR(c(1,10))
##[1] 10 19


[Package GeneR version 2.24.0 Index]