seqSkew {GeneR}R Documentation

compute the strand assymetries from one sequence fragment

Description

compute the strand assymetries from one sequence fragment

Usage

seqSkew(seqno = 0, from=1,to=0,strand=getStrand(),case = "all")
GCcontent(seqno = 0, from=1,to=0,case = "all",...)

Arguments

seqno

Input sequence number. (bufseq)

from,to

Begining and ending of sequence, can be vectors. 0 represent the last nucleotide and 1 the first one.

case

"all"

strand

strand

...

other parameters

Value

a data frame with 4 columns as follow

TA skew or TA pourcent

(T-A)/(T+A) or count(TA) / count(TAGCN)

GC skew or GC pourcent

(G-C)/(G+C) or count(GC) / count(TAGCN)

total skew or C pourcent

TA+GC skews or count(C) / count(TAGCN)

Author(s)

Yves d'Aubenton and Emna

See Also

densityProfile,bankDensityProfile,compoSeq

Examples

     s<-"CGTACGTAGTAGCTAGCTAGCTAGCTAGCTGATCGATGCTAGCTGATCGATGCT"
     placeString(s,seqno=0)
     x<-c(1,8,15,50)
     y<-c(5,12,19,54)
     seqSkew(seqno=0,from=x,to=y,strand=0)

     seqSkew(seqno=0,from=x,to=y,strand=1)

     GCcontent(seqno=0,from=x,to=y)




[Package GeneR version 2.24.0 Index]