mlda.data {MLDA}R Documentation

Generate a data set in mlda

Description

A function to generate a dataset object in MLDA

Usage

mlda.data(dig1, undig1, dig2, undig2, unmeth.flag, cl, sample.names = NULL, 
                                        flag1 = NULL, flag2 = NULL)

Arguments

dig1 log-transformed signal intensities for digested samples in DMH
undig1 log-transformed signal intensities for undigested samples in DMH
dig2 log-transformed signal intensities for digested samples in DMH on dye-swapped/duplicated array
undig2 log-transformed signal intensities for undigested samples in DMH on dye-swapped/duplicated array
unmeth.flag flag for unmethylated controls
cl class of samples (class 1 and class 2)
sample.names sample labels
flag1 flag for the probes with low quality
flag2 flag for the probes with low quality on dye-swapped/duplicated arrays

Value

a list containing:

R A matrix of log-transformed signal intensities for undigested samples in DMH
G A matrix of log-transformed signal intensities for digested samples in DMH
Rds A matrix of log-transformed signal intensities for digested samples in DMH on dye-swapped/duplicated array
Gds A matrix of log-transformed signal intensities for undigested samples in DMH on dye-swapped/duplicated array
mito.flag A vector of flag for unmethylated controls
cl A vector of class labels for samples
sample.names sample labels
flag A matrix of flag for the low quality probes
flagds A matrix of flag for the low quality probes on dye-swapped/duplicated arrays

Author(s)

Wei Dai w.dai@imperial.ac.uk

Examples


data(hcgi12k)
i<-c(1,5)
dataset<-mlda.data(dig1=hcgi12k$G[,i],undig1=hcgi12k$R[,i],
dig2=hcgi12k$Rds[,i],undig2=hcgi12k$Gds[,i],
unmeth.flag=hcgi12k$mito.flag,cl=hcgi12k$cl[i],
sample.names=hcgi12k$sample.names[i],
flag1=hcgi12k$flag[,i],flag2=hcgi12k$flagds[,i])
                

[Package MLDA version 1.0-1 Index]