plotCVBoxes: Boxplots of CV for qPCR Ct values.

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/plotCVBoxes.R

Description

Function that will calculate the coefficients of variation across selected qPCR data, and plot the results in a boxplot.

Usage

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plotCVBoxes(q, cards = TRUE, xlab = "", ylab = "CV", col = brewer.pal(5, "Spectral"), main = NULL, stratify, ...)

Arguments

q

object of class qPCRset.

cards

vector, the numbers of the cards to plot. Defaults to TRUE = all cards.

xlab

character string, label for the x-axis.

ylab

character string, label for the y-axis.

col

vector of colours to use.

main

character string, plot title.

stratify

character, specifying what to stratify the Ct values by. NULL, the default means no stratification, "type" is the feature types of the qPCRset, and "class" the feature class.

...

any other arguments will be passed to the boxplot function.

Details

The CV is calculated across all the selected cards based on each well position, without taking possibly replicated genes on the cards into consideration. "type" and "class" are automatically extracted from the qPCRset using featureType and featureClass.

Value

A plot is created on the current graphics device. The CV values are returned invisibly.

Author(s)

Heidi Dvinge

See Also

boxplot

Examples

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# Load example data
data(qPCRraw)
# Make plot with all samples or just a few
plotCVBoxes(qPCRraw)
plotCVBoxes(qPCRraw, cards=c(1,4))
plotCVBoxes(qPCRraw, stratify="class")
x <- plotCVBoxes(qPCRraw, stratify="type")
x[1:10]

HTqPCR documentation built on Nov. 1, 2018, 2:23 a.m.