getDeseqRes: Differential circRNA expression analysis adapted from DESeq2

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

Differential circRNA expression analysis adapted from DESeq2

Description

The helper functions getDeseqRes() identifies differentially expressed circRNAs. The latter uses respectively the R Bioconductor packages DESeq2 which implements a beta-binomial model to model changes in circRNA expression.

Usage

getDeseqRes(
  backSplicedJunctions,
  condition,
  pAdjustMethod = "BH",
  pathToExperiment = NULL,
  ...
)

Arguments

backSplicedJunctions	A data frame containing the back-spliced junction coordinates and counts in each analyzed sample. See getBackSplicedJunctions and mergeBSJunctions (to group circRNA detected by multiple detection tools) on how to generated this data frame.
condition	A string specifying which conditions to compare. Only 2 conditions at the time can be analyzed. Separate the 2 conditions with a dash, e.g. A-B. Use the same name used in column condition in experiment.txt. log2FC calculation is perfomed by comparing the condition positioned forward against the condition positioned backward in the alphabet. E.g. if there are 2 conditions A and B then a negative log2FC means that in condition B there is a downregulation of the corresponding circRNA. If a positive log2FC is found means that there is an upregulation in condition B of that circRNA.
pAdjustMethod	A character string stating the method used to adjust p-values for multiple testing. See p.adjust. Deafult value is "BH".
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.
...	Arguments to be passed to the DESeq function used internally from DESeq2 package. If nothing is specified the default values of the function DESeq are used.

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)

# Find differentially expressed circRNAs
deseqResBvsA <- getDeseqRes(
    filteredCirc,
    condition = "A-B",
    pAdjustMethod = "BH",
    pathToExperiment)

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