source('selectValidBarcodes.R')
dim(bc)
X11()
colnames(bc)
source('selectValidBarcodes.R')
plot(bc$count,pch=20,log='y',xlab='BC index',ylab='reads per barcode',cex=0.5)
abline(h=10000,lty=3,col='red')
bcThresh <- 10000
nValidBc <- length(which(bc$count>bcThresh))
nValidBc
fractValid <- sum(bc$count[which(bc$count>bcThresh)])/sum(bc$count)
fractValid
print(sprintf('Valid barcodes: %d, %4.2f useable reads', nValidBc, fractValid))
print(sprintf('Valid barcodes: %d, %4.2f%% of total reads', nValidBc, fractValid*100))
dev.set(dList[2])
bc.sort <- sort(bc$count)
plot(bc.sort,type='l',log='y',xlab='barcode count rank (low-to-high)',ylab='reads per barcode')
length(which(bc.sort<bcThresh))
abline(v=140261,lty=3,col='red')
nBc <- length(bc.sort)   # total # of barcodes
plot((nBc-5000):nBc,bc.sort[(nBc-5000):nBc],log='y',xlab='barcode count rank (low-to-high)',ylab='reads per barcode',main='top 5000 barcodes')
nBc <- length(bc.sort)   # total # of barcodes
plot((nBc-5000):nBc,bc.sort[(nBc-5000):nBc],log='y',xlab='barcode count rank (low-to-high)',ylab='reads per barcode',main='top 5000 barcodes',type='l')
abline(v=length(which(bc.sort<=bcThresh)),lty=3,col='red')
abline(v=141000,lty=3,col='red')
abline(v=140500,lty=3,col='red')
bc.sort[140500]
bc.sort[140400]
bc.sort[140400]
abline(v=140400,lty=3,col='red')
dev.set(2)
abline(h=20000)
source('selectValidBarcodes.R')
source('selectValidBarcodes.R')
quit()
n
