CountsBio: CountsBio class

In SoniaTC/NOISeq: Exploratory analysis and differential expression for RNA-seq data

Description

CountsBio class generated from dat() function with type="countsbio". This object contains the count distribution for each biological group and also the percentage of features with counts per million higher than 0, 1, 2, 5 or 10, per each sample independently and in at least one of the samples (total).

Usage

## S4 method for signature 'CountsBio'
explo.plot(object, samples = c(1,2), toplot = "global", plottype = c("barplot", "boxplot"),...)
## S4 method for signature 'CountsBio'
dat2save(object)

Arguments

object	Object generated with dat() function.
toplot	This parameter indicates which biological group is to be plotted. It may be a number or a text with the name of the biological group. If toplot=1 (or "global"), a global plot with all the biological groups will be generated.
samples	Samples or conditions to be plotted. If NULL, the two first samples are plotted because the plot for this object only admit a maximum of two samples.
plottype	Type of plot to be generated for "countsbio" data. If "barplot", the plot indicates the percentage of features with counts per millior higher than 0, 1, 2, 5 or 10 counts or less. Above each bar, the sequencing depth (million reads) is shown. If "boxplot", a boxplot is drawn per sample or condition showing the count distribution for features with more than 0 counts. Both types of plot can be obtained for all features ("global") or for a specified biotype (when biotypes are available).
...	Any argument from par.

Slots/List Components

Objects of this class contain a list (dat) with the following components:

result: Matrix containing the expression data for all the detected features and all samples or conditions.

bionum: Vector containing the number of detected features per biological group (global indicates the total).

biotypes: Vector containing the biological group (biotype) for each detected feature.

summary: List with as many elements as number of biotypes and an additional element with the global information (for all features). Each element is a data frame containing for each sample or condition the number of features with 0 counts, 1 count or less, 2 counts or less, 5 counts or less and 10 counts or less, more than 10 counts, the total number of features and the sequencing depth.

Methods

This class has an specific show method in order to work and print a summary of the elements which are contained and a dat2save method to save the relevant information in an object cleanly. It also has an explo.plot method to plot the data contained in the object.

Author(s)

Sonia Tarazona

SoniaTC/NOISeq documentation built on July 28, 2020, 6:31 p.m.