percCellQualControl {RNAither} | R Documentation

## Quality control of the percentage of cells

### Description

Plots a histogram of the percentage of cells per well (ratio of the number of identified cells and the number of identified objects) and allows the user to set an upper and a lower threshold so as to exclude wells from the analysis.

### Usage

    percCellQualControl(DataSetFile, nbLinesHeader, plotTitle)

### Arguments

`DataSetFile` | a dataset file generated with `generateDatasetFile`
`nbLinesHeader` | typically 3
`plotTitle` | the plot title

### Value

Prints out the list of wells under and over the predefined thresholds in the shell.

Saves a list of discarded siRNA values (if applicable) in a text file named after the experiment name specified in the header concatenated with either "percCellQualControl\_discarded\_higher.txt" or "percCellQualControl\_discarded\_lower.txt".

Saves the histogram with the applied thresholds in a pdf file named after the experiment name specified in the header concatenated with the `plotTitle`.

Overwrites the given `DataSetFile` with the new dataset.

### See Also

`numCellQualControl`

### Examples

    data(exampleHeader, package="RNAither")
    data(exampleDataset, package="RNAither")
    saveDataset(header, dataset, "save_testfile1.txt")

    percCellQualControl("save_testfile1.txt", 3, "Histogram of the number of cells")

[Package RNAither version 2.36.0 Index]