qualityControl: Quality control plots

In aursiber/kissDE: Retrieves Condition-Specific Variants in RNA-Seq Data

Quality control plots

Description

Function that provide some helpful plots about the data to ensure that the experimental plan passed to diffExpressedVariants is correct and to control the quality of the data. This function should be run before launching diffExpressedVariants, to validate the data.

Usage

qualityControl(countsData, conditions, storeFigs = FALSE, returnPCAdata = FALSE)

Arguments

countsData	the output of the kissplice2counts function or a data frame containing the counts in the appropriate format (see Details below).
conditions	a character vector that gives the conditions' order. It has as many elements as there are samples in total.
storeFigs	a logical or a string indicating if the plots should be stored and in which directory. If the qualityControl function is a part of an automatised worflow, we recommand to set this option to TRUE or to a user defined value. If storeFigs is TRUE, the figures will be stored in a kissDEFigures directory which is created in a temporary directory. This directory will be removed when the R session is closed. If storeFigs is a path (a string, e.g. '/path/to/figs'), this directory is created to store the figures. Note that if the directory already exist, it will be overwritten. Plots are stored in .png format. By default (FALSE), the interactive mode is enabled and plots are returned to the graphics device.
returnPCAdata	a logical indicating if the data frame used in the PCA analysis should be returned. By default (FALSE), the data frame is not returned.

Details

countsData input must be formatted as follows: in its first column the names of the events, in its second column the lengths of the events, and in the following columns, the counts corresponding to each replicate of each experimental condition of one variant. Each row corresponds to one variant.

Value

The figures are saved or displayed in the R session.

See Also

diffExpressedVariants

Examples

fpath <- system.file("extdata", "output_kissplice_SNV.fa", package="kissDE")
mySNVcounts <- kissplice2counts(fpath, counts = 0, pairedEnd=TRUE)
mySNVconditions <- c("EUR", "EUR", "TSC", "TSC")
qualityControl(mySNVcounts, mySNVconditions)

aursiber/kissDE documentation built on Jan. 28, 2024, 10:01 a.m.