filterCirc: Filter circRNAs

In Aufiero/circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

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)

Aufiero/circRNAprofiler documentation built on Nov. 3, 2024, 10:12 a.m.