scan-class {inveRsion} | R Documentation |
Results from scanning the genome with the inversion model for trial segments of fixed window size.
scan
objects are typically generated by callings to the constructor function scanInv
leftBP
:Object of class "matrix"
Left brake-point coordinates (right SNP)
rightBP
:Object of class "matrix"
Right brake-point coordinates (right SNP)
leftBP2
:Object of class "matrix"
Left brake-point coordinates (left SNP)
rightBP2
:Object of class "matrix"
Right brake-point coordinates (right SNP)
LogLike
:Object of class "matrix"
Log-likelihood ratio for each trial segment
prob
:Object of class "matrix"
probability of no-inversion for each trial segment
ent
:Object of class "matrix"
entropy for each trial segment
entTh
:Object of class "matrix"
entropy threshold for each trial segment
bic
:Object of class "matrix"
BIC for each trial segment
window
:Object of class "numeric"
window size
signature(object = "scan")
: gets scan results into a matrix
signature(object = "scan")
: get regions of interest, overlapping trial segments with significant BIC
signature(object = "scan")
: determines the inversion sequence for each ROI
signature(x = "scan")
: plots scan
results, set option which=c("bic","log","prob","ent")
to plot BIC, log-likelihood ratio, probability of no inversion or entropy; and thBic=0
to plot segments with BIC greater than 0
signature(object = "scan")
: shows scan results for each ROI
Alejandro Caceres acaceres@creal.cat
listInv
, HaploCode
, getInv
, getROIs
data(scanRes) scanRes plot(scanRes,which="bic",thBic=0)