R/bscon_methy.R

In schalkwyk/wateRmelon: Illumina DNA methylation array normalization and metrics

#New BScon_methy after modifications of 17.09.2015

bscon_methy <- function(mset450k) {

green.Channel <- try (intensitiesByChannel(QCdata(mset450k))$Cy3, silent = T)
if (!inherits (green.Channel, 'try-error')){green.Channel <- intensitiesByChannel(QCdata(mset450k))$Cy3} 
  else 
    stop ("Green channel 450k QC data could not be found")

red.Channel<-try (intensitiesByChannel(QCdata(mset450k))$Cy5, silent = T)
if (!inherits (red.Channel, 'try-error')){red.Channel <- intensitiesByChannel(QCdata(mset450k))$Cy5} 
else 
  stop ("Red channel 450k QC data could not be found")

rownames(green.Channel)-> green.rows
rownames(red.Channel)-> red.rows
#   Old Regex: "^B.*C.*I" #  find any rownames starting with B that contain a subsequent C and then an I
bisulfite.green <- green.Channel[grep("(^B.*C.*)\\bI\\b.*", rownames(green.Channel)),] 
bisulfite.red <- red.Channel[grep("(^B.*C.*)\\bI\\b.*", rownames(red.Channel)),]
  
bsI.green <- bisulfite.green #[1:12,]
bsI.red <- bisulfite.red #[1:12,]
bsII.green <- green.Channel[grep("(^B.*C.*)\\bII\\b.*", rownames(green.Channel)),]    #  as above with II (subset of above)
bsII.red <- red.Channel[grep("(^B.*C.*)\\bII\\b.*", rownames(red.Channel)),]
  
# calculate BS conv type 1 betas as an example of using an index vector
if(nrow(bsI.green) > 11){ # 450K
  BSI.betas <- rbind(bsI.green[1:3,], bsI.red[7:9,])/((rbind(bsI.green[1:3,], bsI.red[7:9,])) + rbind(bsI.green[4:6,], bsI.red[10:12,]))
} else { # EPIC (Skip the missing probe pair...)
  BSI.betas <- rbind(bsI.green[1:2,], bsI.red[6:7,])/((rbind(bsI.green[1:2,], bsI.red[6:7,])) + rbind(bsI.green[3:4,], bsI.red[ 8:9 ,]))
}
#calculation of BS conv in Type II data
BSII.betas <- bsII.red/(bsII.red + bsII.green)
apply(rbind(BSI.betas, BSII.betas), 2, median)*100 ## this is the value you are interested in 
}