getEdgerRes: Differential circRNA expression analysis adapted from EdgeR

Description Usage Arguments Value Examples

View source: R/getEdgerRes.R

Description

The helper functions edgerRes() identifies differentially expressed circRNAs. The latter uses respectively the R Bioconductor packages EdgeR which implements a beta-binomial model to model changes in circRNA expression. The info reported in experiment.txt file are needed for differential expression analysis.

Usage

1
2
3
4
5
6
7
getEdgerRes(
  backSplicedJunctions,
  condition,
  normMethod = "TMM",
  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.

normMethod

A character string specifying the normalization method to be used. It can be "TMM","RLE","upperquartile" or"none". The value given to the method argument is given to the calcNormFactors used internally. Deafult value is "TMM".

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.

Value

A data frame.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
# 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 <- getEdgerRes(
    filteredCirc,
    condition = "A-B",
    normMethod = "TMM",
    pAdjustMethod = "BH",
    pathToExperiment)

Aufiero/circRNAprofiler documentation built on July 22, 2021, 9:34 p.m.