README.md

In markziemann/Mitch: Multi-Contrast Gene Set Enrichment Analysis

mitch

mitch is an R package for multi-dimensional enrichment analysis. At it's heart, it uses a rank-MANOVA based statistical approach to detect sets of genes that exhibit enrichment in the multidimensional space as compared to the background. Mitch is useful for pathway analysis of profiling studies with two to or more contrasts, or in studies with multiple omics profiling, for example proteomic, transcriptomic, epigenomic analysis of the same samples. Mitch is perfectly suited for pathway level differential analysis of scRNA-seq data.

Installation

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("mitch")

library("mitch")

Workflow overview

Importing gene sets

mitch has a function to import GMT files to R lists (adapted from Yu et al, 2012 in the clusterProfiler package). For example:

download.file("https://reactome.org/download/current/ReactomePathways.gmt.zip", destfile="ReactomePathways.gmt.zip")
unzip("ReactomePathways.gmt.zip")
genesets <- gmt_import("ReactomePathways.gmt")

Importing profiling data

mitch accepts pre-ranked data supplied by the user, but also has a function called mitch_import for importing tables generated by Limma, edgeR, DESeq2, ABSSeq, Sleuth, Seurat and Muscat. By default, only the genes that are detected in all contrasts are included, but this behaviour can be modified. The below example imports two edgeR tables called "dge1" and "dge2". Where gene identifiers are coded in the row names.

x <- list("dge1"=dge1, "dge2"=dge2)
y <- mitch_import(x, DEtype="edger")

mitch can do unidimensional analysis if you provide it a single profile as a dataframe.

y <- mitch_import(df, DEtype="edger")

If the gene identifiers are not given in the rownames, then the column can be specified with the geneIDcol parameter like this:

y <- mitch_import(df, DEtype="edger", geneIDcol="MyGeneIDs")

By default, differential gene activity is scored using the directional nominal p-value.

S = -log10(p-value) * sgn(logFC)

If this is not desired, then users can perform their own custom scoring procedure.

There are many cases where the gene IDs don't match the gene sets. To overcome this, mitch_import also accepts a two-column table that relates gene identifiers in the profiling data to those in the gene sets.

?mitch_import provides more instructions on using this feature.

Calculating enrichment

The mitch_calc function performs multivariate enrichment analysis of the supplied gene sets in the scored profiling data. At its simpest form mitch_calc function accepts the scored data as the first argument and the genesets as the second argument. Users can prioritise enrichments based on small adjusted p-values, or by the observed effect size (magnitude of the enrichment score).

res <- mitch_calc(y, genesets, priority="significance")
res <- mitch_calc(y, genesets, priority="effect")

You can peek at the top results with head like this:

head(res$enrichment_result)

By default, mitch_calc uses mclapply to speed up calculations on all but one available CPU threads. This behaviour can be modified by setting the cores to a desred number.

res <- mitch_calc(y, genesets, priority="significance", cores=4)

By default, gene sets with fewer than 10 members present in the profiling data are discarded. This threshold can be modified using the minsetsize option. There is no upper limit of gene set size.

res <- mitch_calc(y, genesets, priority="significance", minsetsize=20)

By default, in downstream visualisation steps, charts are made from the top 50 gene sets, but this can be modified using the resrows option.

res <- mitch_calc(y, genesets, priority="significance", resrows=100)

Generate a HTML report

Can be done like this:

mitch_report(res, "myreport.html")

Take a look at an example report.

Generate high resolution plots

In case you want the charts in PDF format, these can be generated as such:

mitch_plots(res, outfile="mycharts.pdf")

Take a look at an example plot set.

scRNA-seq

This type of data is notoriously sparse. Mitch works best if there are >1000 genes detected in each cell type (contrast). If there are <400 genes present it may cause mitch to run into an error in the MANOVA test due to insufficient degrees of freedom.

Infinium DNA methylation data

Mitch can be applied to Infinium Beadarray methylation data if you have limma results for probes. Please see our solution described at our other repository.

Contrbutions

If you have questions or need help with applying mitch to your work, please raise an issue.

markziemann/Mitch documentation built on Nov. 2, 2024, 3:12 a.m.