plotCtSignificance: Barplot with Ct values between genes from qPCR.

Description Usage Arguments Details Value Author(s) See Also

View source: R/plotCtSignificance.R

Description

Function for producing a barplot of the Ct values from high-throughput qPCR samples. A comparison is made between two groups which have been tested for differential expression, and all individual Ct values are shown, to identify potential outliers.

Usage

1
plotCtSignificance(qDE, q, comparison = 1, genes, p.val = 0.1, groups, calibrator, target, p.sig = 0.05, p.very.sig = 0.01, mark.sig = TRUE, col, un.col = "#D53E4F", point.col = "grey", legend = TRUE, mar, main, jitter = 0.5, ...)

Arguments

qDE

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

q

the qPCRset data that was used for testing for differential expression.

comparison

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

genes

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

p.val

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

groups

vector, the groups of all the samples in q.

calibrator

character string, which of the groups is the calibrator.

target

character string, which of the groups is the target.

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.sig

logical, should significant features be marked.

col

vector, colours to use for the two sets of bars, one per sample type.

un.col

integer or character string, the colour to use for all Ct values that are "Unreliable" or "Undetermined".

point.col

integer or character string, the colour to use for all other Ct values.

legend

logical, should a legend be included int eh barplot.

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.

jitter

numeric, between 0 and 1. If Ct values are very similar, the individual points might lie on top of each other in the bars. This adds a jittering factor along the x-axis. If 0 the points will all be aligned.

...

any other arguments will be passed to the barplot function.

Details

This function will make a barplot with the average Ct values for the test and reference samples for the selected genes. All the individual Ct values are plotted on top of the bars though, and the "Unreliable" or "Undetermined" ones are marked, to do a visual assessment of the impact of non-valid measurements on the average.

It's up to the user to specify the correct calibrator and target for the given comparison; no checking is done.

Value

A plot is created on the current graphics device.

Author(s)

Heidi Dvinge

See Also

barplot and plotCtRQ or plotCtOverview for a plot of the relative quantification between samples.


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