addMaxEnt {spliceSites} | R Documentation |
addMaxEnt adds new columns to object data which contain
MaxEnt-Score derived values.
mxe_ps5
contains score5
values for left align-gap (exon-intron)
boundary (i.e. assumed to reside on '+'-strand. mxe_ps3
contains
score3
(maxent) values for right align-gap (intron-exon) boundary
(i.e. assumed to reside on '+'-strand).
mxe_ms5
contains score5
values for right align-gap (exon-intron)
boundary on reverseComplement
transformed sequence (i.e. assumed to
reside on '-'-strand).
mxe_ms3
contains score3
values for left align-gap (intron-exon)
boundary on reverseComplement
transformed sequence (i.e. assumed to
reside on '-'-strand).
From these values, s3strand
, s5strand
and meStrand
are derived: s3strand
is '+' when mxe_ps5
>= mxe_ms5
and '-' otherwise; s3strand
is '+' when
mxe_ps3
>= mxe_ms3
and '-' otherwise.
meStrand
equals s5strand
when s5strand
=s3strand
and '*' otherwise.
The function setMeStrand
copies existing meStrand
values
into strand
column (and throws an error when meStrand
does not exist).
addMaxEnt(x,dna,maxent,digits=1)
x |
gapSites. |
dna |
DNAStringSet. Reference sequence identifier. |
maxent |
maxEnt. Contains score table which are internally
used by |
digits |
Numeric. Default value: 1. Internally calculated maxent scores are rounded to given number of decimal places. |
gapSites
Wolfgang Kaisers
# A) Read gapSites bam<-system.file("extdata","rna_fem.bam",package="spliceSites") reader<-bamReader(bam,idx=TRUE) ga<-alignGapList(reader) bamClose(reader) # B) Load DNA dnafile<-system.file("extdata","dna_small.RData",package="spliceSites") load(dnafile) # C) maxEnt mes<-load.maxEnt() gae<-addMaxEnt(ga,dna_small,mes) getMeStrand(gae) sae<-setMeStrand(gae)