freq2p: Compute the Frequencies in an Alignment
In BioPhysConnectoR: BioPhysConnectoR

Description Usage Arguments Details Value Author(s) References See Also Examples

One and two point frequencies of a specified column or specified columns are computed for a given alignment.

1
2
3

freq1p(aln, i = NULL)

freq2p(i, aln, j2 = NULL, lett = NULL, cluster = NULL)

`aln`	alignment
`i`	reference column for the frequency computation
`j2`	columns to compute the two point frequency together with column `i`
`lett`	character vector containing the unique alphabet of the alignment
`cluster`	snow cluster object created with `makeCluster()`

The columns j2 are the specified columns (not i) to compute the frequencies and the rows represent all possible two letter pairs according to the alphabet. The computation of freq2p() is parallelized using parLapply() from the package snow. If cluster is left at its default value the computation is carried out in serial.

A matrix is returned for the freq2p(). For freq1p(), if no i is specified, a matrix containing the frequencies of the symbols in the alignment is returned. For a certain i a vector with the respective frequencies of the symbols is the result.

Franziska Hoffgaard, Philipp Weil

Tierney, Rossini, Li (2009) Int J Parallel Proc 37, 78–90.

get.entropy, get.mie

seqa<-unlist(strsplit("PQITLWQRPLVTIKIGGQL",split=""))
seqb<-unlist(strsplit("PQITLWKRPLVTIRIGGQL",split=""))
seqc<-unlist(strsplit("PQITLWQRPLVTIKIGGQL",split=""))
aln<-matrix(c(seqa,seqb,seqc),nrow=3,byrow=TRUE)
f1<-freq1p(aln)
f1a<-freq1p(aln, 1)
f2<-freq2p(1, aln, 2:10)
## Not run: 
## Cluster example
clu<-makeCluster(2)
f2<-freq2p(1, aln, 2:10, cluster=clu)
stopCluster(clu)

## End(Not run)