In chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data

MFIaggr - report

Date: r Sys.time()

MFIaggr analysis

x <- res.mfi()
summary(x)
plot(x)

Table

library(knitr)
tab.dat <- slot(x, ".Data")
tab.dat <- data.frame(tab.dat)
tab.dat[["Cycle"]] <- as.factor(tab.dat[["Cycle"]])
kable(tab.dat, format = "markdown", align = c("r", "c", "c", "c"), padding = 2)

All curves plot

dat <- processed.data()
plotCurves(dat[[input[["cyc.col"]]]], dat[, -input[["cyc.col"]]], CPP = TRUE, type = "l")

Settings used during analysis

cat("Input file name: ", ifelse(is.null(input[["input.file"]][["name"]]), 
                                        "example", input[["input.file"]][["name"]]), "\n\n")
cat("Column containing the cycle data: ", input[["cyc.col"]], "\n\n")
cat("Relative standard deviation: ", input[["RSD"]], "\n\n")
cat("Median and MAD: ", input[["rob"]], "\n\n")
cat("Region of interest - lower border: ", input[["llul.low"]], "\n\n")
cat("Region of interest - upper border: ", input[["llul.up"]], "\n\n")

chipPCR documentation built on March 5, 2021, 9:06 a.m.