plotMA.CD: 'MA'-plot for count data.

In baySeq: Empirical Bayesian analysis of patterns of differential expression in count data

Description

This function creates an MA-plot from two sets of samples. For those data where the log-ratio is infinite (because in one set of sample data all observed counts are zero), we plot instead the log-values of the other group.

Usage

plotMA.CD(cD, samplesA, samplesB, normaliseData = TRUE, scale = NULL,
xlab = "A", ylab = "M", ...)

Arguments

cD	A countData object.
samplesA	Either a character vector, identifying sample set A by either replicate name or sample name, or a numerical vector giving the columns of data in the 'countData' object that forms sample set A. See Details.
samplesB	Either a character vector, identifying sample set B by either replicate name or sample name, or a numerical vector giving the columns of data in the 'countData' object that forms sample set B. See Details.
normaliseData	Should the data be normalised by library size before computing log-ratios? Defaults to TRUE.
scale	If given, defines the scale on which the log-ratios will be plotted. Defaults to NULL, implying that the scale will be calculated by the function.
xlab	Label for the X-axis. Defaults to "A".
ylab	Label for the Y-axis. Defaults to "M".
...	Any other parameters to be passed to the plot function.

Details

The samples sets can be identified either by a numeric vector which specifies the columns of data from the countData object 'cD', or by a character vector. If a character vector is used, the members of the character vector will first be searched for in the @replicates slot of the 'cD' object. Any members of the vector not found in the replicates slot, will be searched for in the column names of the @data slot of the 'cD' object. Different classes of vector can be used for 'samplesA' and 'samplesB', as shown in the example below.

Value

Plotting function.

Author(s)

Thomas J. Hardcastle

See Also

countData

Examples

data(simData)

replicates <- c("simA", "simA", "simA", "simA", "simA", "simB", "simB", "simB", "simB", "simB")
groups <- list(NDE = c(1,1,1,1,1,1,1,1,1,1), DE = c(1,1,1,1,1,2,2,2,2,2))
CD <- new("countData", data = simData, replicates = replicates, groups = groups)

#estimate library sizes for countData object
libsizes(CD) <- getLibsizes(CD)

#MA-plot comparing replicate groups
plotMA.CD(CD, samplesA = "simA", samplesB = 6:10)

baySeq documentation built on Nov. 8, 2020, 5:43 p.m.