filterCirc: Filter circRNAs

Description Usage Arguments Value Examples

View source: R/filterCirc.R

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

1
2
3
4
5
6
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
# 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 July 22, 2021, 9:34 p.m.