QtoJackson: Q to Jackson: transform a Q-residual into a confidence...

In MEET: MEET: Motif Elements Estimation Toolkit

Description

Given Q-residual, this function uses the parameters calculated in JAcksonParameters to convert a Q-residual into a confidence interval

Usage

QtoJackson(Q,h0, x1, x2, x3)

Arguments

Q	Q-residual
h0	h0 parameter
x1	x1 parameter
x2	x2 parameter
x3	x3 parameter

Value

output:confidence interval of the given residual.

Author(s)

Erola Pairo <epairoatibec.pcb.ub.es>

See Also

kfold.PCA, Predict.PCA, JacksonParameters

Examples

require("MEET")
data(TranscriptionFactor)
data(iicc)
nPCs<-1
TFBS<-iicc$Transcriptionfactor
Prob<-iicc$background
missing<-iicc$missing
NumericalMatrix<-numericalDNA(Prob)
suma<-apply(TFBS,2,function(y){sum(y=="-")})
threshold<-floor(nrow(TFBS)*missing/100)
TFBS<-TFBS[, suma<=threshold]
ncolTFBS<-ncol(TFBS)
TFBSnum<-apply(TFBS,1,function(x){as.vector(t(NumericalMatrix[x,]))})
TFBSnum<-t(TFBSnum)
model<-pca(TFBSnum, nPcs=2, method="svd", center=TRUE)
JacksonPars<-JacksonParameters(nPCs,TFBSnum)
Qres<-3.45
confidence<-QtoJackson(Qres,h0=1,x1=1,x2=1,x3=1)

MEET documentation built on May 2, 2019, 1:45 p.m.