filterCirc {circRNAprofiler} | R Documentation |
The functions filterCirc() filters circRNAs on different criteria: condition and read counts. The info reported in experiment.txt file are needed for filtering step.
filterCirc( backSplicedJunctions, allSamples = FALSE, min = 3, pathToExperiment = NULL )
backSplicedJunctions |
A data frame containing back-spliced junction
coordinates and counts. See |
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:
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. |
A data frame.
# 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)