RDML.SetFData | R Documentation |
RDML
objectSets fluorescence data vectors to RDML
object for specified method
of experiment.
data |
|
description |
output from |
fdata.type |
'adp' for qPCR, 'mdp' for melting data. |
## Not run: PATH <- path.package("RDML") filename <- paste0(PATH, "/extdata/", "stepone_std.rdml") cfx96 <- RDML$new(filename) ## Use plotCurves function from the chipPCR package to ## get an overview of the amplification curves library(chipPCR) ## Extract all qPCR data tab <- cfx96$AsTable() tab2 <- tab tab2$run.id <- "cpp" cfx96.qPCR <- as.data.frame(cfx96$GetFData(tab)) cpp <- cbind(cyc = cfx96.qPCR[, 1], apply(cfx96.qPCR[, -1], 2, function(y) CPP(x = cfx96.qPCR[, 1], y = y)$y.norm)) cfx96$SetFData(cpp, tab2) library(ggplot2) library(gridExtra) cfx96.gg <- cfx96$GetFData(tab, long.table = TRUE) cpp.gg <- cfx96$GetFData(tab2, long.table = TRUE) plot1 <- ggplot(cfx96.gg, aes(x = cyc, y = fluor, group=fdata.name)) + geom_line() + ggtitle("Raw data") plot2 <- ggplot(cpp.gg, aes(x = cyc, y = fluor, group=fdata.name)) + geom_line() + ggtitle("CPP processed data") grid.arrange(plot1, plot2, nrow=2) ## End(Not run)
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