filterCirc {circRNAprofiler} | R Documentation

## Filter circRNAs

### Description

The functions filterCirc() filters circRNAs on different criteria: condition and read counts. The info reported in experiment.txt file are needed for filtering step.

### Usage

    filterCirc(
      backSplicedJunctions,
      allSamples = FALSE,
      min = 3,
      pathToExperiment = NULL
    )

### Arguments

`backSplicedJunctions` | A data frame containing back-spliced junction coordinates and counts. See `getBackSplicedJunctions` and `mergeBSJunctions` (to group circRNA detected by multiple detection tools) on how to generated this data frame.
`allSamples` | A string specifying whether to apply the filter to all samples. Default valu is FALSE.
`min` | An integer specifying the read counts cut-off. If allSamples = TRUE and min = 0 all circRNAs are kept. If allSamples = TRUE and min = 3, a circRNA is kept if all samples have at least 3 counts. If allSamples = FALSE and min = 2 the filter is applied to the samples of each condition separately meaning that a circRNA is kept if at least 2 counts are present in all sample of 1 of the conditions. Default value is 3.
`pathToExperiment` | A string containing the path to the experiment.txt file. The file experiment.txt contains the experiment design information. It must have at least 3 columns with headers: label: (1st column) - unique names of the samples (short but informative). fileName: (2nd column) - name of the input files - e.g. circRNAs_X.txt, where x can be can be 001, 002 etc. group: (3rd column) - biological conditions - e.g. A or B; healthy or diseased if you have only 2 conditions. By default pathToExperiment is set to NULL and the file it is searched in the working directory. If experiment.txt is located in a different directory then the path needs to be specified.

### Value

A data frame.

### Examples

    # Load a data frame containing detected back-spliced junctions
    data("mergedBSJunctions")

    pathToExperiment <- system.file("extdata", "experiment.txt",
        package ="circRNAprofiler")

    # Filter circRNAs
    filteredCirc <- filterCirc(
        mergedBSJunctions,
        allSamples = FALSE,
        min = 5,
        pathToExperiment)

[Package circRNAprofiler version 1.4.2 Index]