seqSkew {GeneR} | R Documentation |
compute the strand assymetries from one sequence fragment
seqSkew(seqno = 0, from=1,to=0,strand=getStrand(),case = "all") GCcontent(seqno = 0, from=1,to=0,case = "all",...)
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 |
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) |
Yves d'Aubenton and Emna
densityProfile
,bankDensityProfile
,compoSeq
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)