CompoSeq {GeneR}R Documentation

Composition in mono, di or trinucleotides of a sequence

Description

Gives composition in mono, di or trinucleotides of fragments of a sequence

Only A, T, G, C are counted, letter as U, X, S, M, N, are counted as 'X'. Flag "case" specify weather we take into acount letters in lower, upper ar all case.

Usage

compoSeq(seqno=0, from=1, to=0, strand=getStrand(),
         wsize=1, p=TRUE,case="all",step=wsize)
strCompoSeq(s, wsize=1, p=TRUE,case="all",step=wsize)

Arguments

seqno

Integer/scalar, Sequence number (buffer number)

s

String/scalar, A sequence as character string

wsize

Integer/scalar, size of k-uples.

from,to

Integer/scalar, Absolute addresses of the beginning and the end of the fragment, (1 means the first nucleotide and 0 conventionally the last one; from must not be larger than to and both vectors must be the same size)

strand

Integer/vector, Strand (forward: 0, reverse: 1)

p

Logical/scalar, If p=TRUE, results are in pourcentages, else, results are in counts.

case

String/scalar, Case of the letters taken into account ("all", "upper", "lower")

step

Integer/scalar, Step increment of positions when counting words.

Value

A matrix with nucleotide composition for all regions (NxM where N = 5*wordSize and M = length(from))

If error: NULL

Note

.Use setStrand by default

See Also

exactWord

Examples

s<-"CGTACGTAGTAGCTAGCTAGCTAGCTAGCTGATCGATGCTAGCTGATCGATGCT"
placeString(s)
x<-c(1,8,15,50)
y<-c(5,12,19,54)
compoSeq(from =x, to = y,wsize=2)

compoSeq(from =x, to = y,wsize=2,strand=1)

compoSeq(from =x, to = y,wsize=2,step=2,p=FALSE)


[Package GeneR version 2.24.0 Index]