Nothing
library(R.utils)
source("01.defineCopyNumberSegments.R")
str(regDat)
datI <- readRDS("CRL2324_dilutionSeries.rds")
datI$posMb <- datI$Position/1e6;
## Define genotypes
pct <- c("100","79", "50", "34", "0")
dataSet <- "CRL2324,BAF"
chipType <- "HumanCNV370v1"
savPath <- "cnRegionData"
savPath <- Arguments$getWritablePath(savPath)
path <- file.path(savPath, dataSet, chipType);
path <- Arguments$getWritablePath(path)
for(pp in pct){
sampleName <- sprintf("CRL2324,BAF,%s",pp)
for (rr in 1:nrow(regDat)) {
chr <- regDat[rr, "chr"]
reg <- c(regDat[rr, "begin"], regDat[rr, "end"])
type <- regDat[rr, "type"]
datCC <- subset(datI, chromosome==chr)
datRR <- subset(datCC, posMb>=reg[1] & posMb<=reg[2])
opos <- order(datRR$posMb)
datRRo <- datRR[opos, ]
datRRo <- na.omit(datRRo)
columns <- c(sprintf("logR_%s",pp), sprintf("baf_%s",pp), "muN")
datSS <- na.omit(datRRo[, columns])
names(datSS) <- c("c","b","genotype")
datSS$c <- 2^(datSS$c + 1)
tgb <- tan(datSS$b*pi/2)
datSS$b <- tgb/(1+tgb)
datSS <- round(datSS, 3)
filename <- sprintf("%s,%s.rds", sampleName, type)
pathname <- file.path(path,filename)
saveRDS(datSS, file=pathname)
}
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.