qualityControl: Quality control plots
In kissDE: Retrieves Condition-Specific Variants in RNA-Seq Data

Description Usage Arguments Details Value See Also Examples

View source: R/qualityControl.R

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.

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

`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.

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.

The figures are saved or displayed in the R session.

diffExpressedVariants

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)