CountsBio {NOISeq} | R Documentation

## CountsBio class

### 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

[Package NOISeq version 2.28.0 Index]