mlda.data {MLDA} | R Documentation |
A function to generate a dataset object in MLDA
mlda.data(dig1, undig1, dig2, undig2, unmeth.flag, cl, sample.names = NULL, flag1 = NULL, flag2 = NULL)
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 |
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 |
Wei Dai w.dai@imperial.ac.uk
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])