plotCtRQ: Plot the relative quantification of Ct values from qPCR...

Description Usage Arguments Details Value Author(s) See Also

View source: R/plotCtRQ.R

Description

Function for plotting the relative quantification (RQ) between two groups of data, whose Ct values have been tested for significant differential expression.

Usage

1
plotCtRQ(qDE, comparison = 1, genes, transform = "log2", p.val = 0.1, mark.sig = TRUE, p.sig = 0.05, p.very.sig = 0.01, mark.un = TRUE, un.tar = "black", un.cal = "black", col, legend = TRUE, xlim, mar, main, ...)

Arguments

qDE

list or data.frame, the result from ttestCtData or limmaCtData.

comparison

integer or character string, indicating which component to use if qDE is a list.

genes

numeric or character vector, selected genes to make the plot for.

transform

character string, how should the data be displayed. Options are "none", "log2" or "log10". See details

p.val

numeric between 0 and 1, if genes is not supplied all given with (adjusted) p-value below this threshold will be included.

mark.sig

logical, should significant features be marked.

p.sig

numeric, the cut-off for significant p-values that will be marked by *.

p.very.sig

numeric, the cut-off for very significant p-values that will be marked by ".

mark.un

logical, should data with unreliable target or calibrator samples be marked. See details.

un.tar

colour to use for the undetermined targets. See details.

un.cal

colour to use for the undetermined calibrators. See details.

col

vector, colours to use for the bars.

legend

logical, should a legend be included in the barplot.

xlim

vector of length 2, the limits on the x-axis. Mainly used for moving the legend to the left of bars.

mar

vector with 4 values, the size of the margins. See par for more info.

main

character string, the image title. Default to the name of the chosen comparison.

...

any other arguments will be passed to the barplot function.

Details

The relative quantification is calculated as RQ=2^-ddCT, where ddCT is the deltadeltaCt value.

If mark.un=TRUE, those bars where either the calibrator or target sample measurements were undetermined are marked using diagonal lines. Whether either of these are called undetermined (includes unreliable values) or not depends on all the input Ct values in ttestCtData or limmaCtData, and whether stringent=TRUE was used in these functions.

Value

A plot is created on the current graphics device.

Author(s)

Heidi Dvinge

See Also

ttestCtData and limmaCtData for testing the Ct data for differential expression.


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