dge_OneFactor: Perform Differential Gene Expression analysis on a one-factor...

In NKInstinct/seqHelpers: Helper Functions for Bulk RNA-Seq Analysis

Perform Differential Gene Expression analysis on a one-factor experiment

Description

This function handles a "default" call of edgeR to perform differential gene expression testing on a count matrix file. The experiment must be a one-factor design (this function isn't set up to handle multi-factor problems yet), but can have any number of levels in that design. You can either specify one reference group to compare all others against, or manually input all comparisons you want it to do. See examples for details.

Usage

dge_OneFactor(
  HitCountsMatrix,
  Groups,
  refGroup = NULL,
  comps = NULL,
  convertNames = FALSE,
  convertFrom = NULL,
  convertTo = NULL,
  retainDGEList = FALSE,
  ...
)

Arguments

HitCountsMatrix	A matrix of hit counts, where each row is a gene and each column is a sample. Note that this should be de-duplicated before running through this function; i.e. each gene should be UNIQUE, and if they aren't you should add the non-unique reads together with dplyr before you start in on this!
Groups	A factor showing what group each sample belongs to. The length of this factor must match the number of columns in the HitCountsMatrix exactly
refGroup	The control group that each other group in the Groups factor will be compared against. If not specified (refGroup = NULL), defaults to the first level in the factor.
comps	A string or character vector giving the comparisons you want to do, in the form of "B-A". Passing a named character vector will give the output the same names.
convertNames	Boolean specifying whether names should be converted. Note that this requires an internet connection, so keep false if you are offline. Typically, this is used to convert the stable Ensembl ID that GeneWiz gives us into a more useful MGI symbol for downstream analysis.
convertFrom	a string specifying a biomart object to convert the names from. Popular choices are "entrezgene_id" and "ensembl_gene_id".
convertTo	a string specifying a biomart object (or character vector for several) to convert names to. Popular choices are "mgi_symbol".
retainDGEList	Boolean specifying whether the DGEList object built by edgeR should be retained and appended to the output (useful for making heatmaps later)
...	Additional arguments to pass to edgeR::filterByExpr. Most likely choices are "min.count", which specifies the minimum number of reads in at least some samples, and "min.total.count", which specifies the minimum number of reads in total, for a gene to be considered.

Value

A dataframe or list of dataframes showing all genes with their fold-change and p value for the specified comparison.

Examples

  data <- system.file("extdata", "sampleMatrix.Rds",
                      package = "seqHelpers") |>
    readRDS()
  grouplist <- factor(c(rep("A", times = 3),
                        rep("B", times = 3),
                        rep("C", times = 3),
                        rep("D", times = 3)))

 # Default comparison, which will compare everything to "A"
 dge_OneFactor(data, Groups = grouplist)

 # Compare everything to D instead
 dge_OneFactor(data, Groups = grouplist, refGroup = "D")

 # Compare B to A and D to C only
 dge_OneFactor(data, Groups = grouplist, comps = c("B" = "B-A",
                                                   "D" = "D-C"))

NKInstinct/seqHelpers documentation built on Aug. 20, 2022, 4:30 a.m.