Perform gene set analysis using zenith

Perform a competitive gene set analysis accounting for correlation between genes.

Usage

# S4 method for dreamletResult,GeneSetCollection
zenith_gsa(
  fit,
  geneSets,
  coefs,
  use.ranks = FALSE,
  n_genes_min = 10,
  inter.gene.cor = 0.01,
  progressbar = TRUE,
  ...
)

# S4 method for dreamlet_mash_result,GeneSetCollection
zenith_gsa(
  fit,
  geneSets,
  coefs,
  use.ranks = FALSE,
  n_genes_min = 10,
  inter.gene.cor = 0.01,
  progressbar = TRUE,
  ...
)

Arguments

fit

results from dreamlet()

geneSets

GeneSetCollection

coefs

coefficients to test using topTable(fit, coef=coefs[i])

use.ranks

do a rank-based test TRUE or a parametric test FALSE? default: FALSE

n_genes_min

minimum number of genes in a geneset

inter.gene.cor

if NA, estimate correlation from data. Otherwise, use specified value

progressbar

if TRUE, show progress bar

...

other arguments

Value

data.frame of results for each gene set and cell type

data.frame of results for each gene set and cell type

Details

This code adapts the widely used camera() analysis (Wu and Smyth 2012) in the limma package (Ritchie et al. 2015) to the case of linear (mixed) models used by variancePartition::dream().

Examples

library(muscat)
library(SingleCellExperiment)

data(example_sce)

# create pseudobulk for each sample and cell cluster
pb <- aggregateToPseudoBulk(example_sce,
  assay = "counts",
  cluster_id = "cluster_id",
  sample_id = "sample_id",
  verbose = FALSE
)

# voom-style normalization
res.proc <- processAssays(pb, ~group_id)
#>   B cells...
#> 0.2 secs
#>   CD14+ Monocytes...
#> 0.33 secs
#>   CD4 T cells...
#> 0.24 secs
#>   CD8 T cells...
#> 0.16 secs
#>   FCGR3A+ Monocytes...
#> 0.32 secs

# Differential expression analysis within each assay,
# evaluated on the voom normalized data
res.dl <- dreamlet(res.proc, ~group_id)
#>   B cells...
#> 0.15 secs
#>   CD14+ Monocytes...
#> 0.21 secs
#>   CD4 T cells...
#> 0.2 secs
#>   CD8 T cells...
#> 0.17 secs
#>   FCGR3A+ Monocytes...
#> 0.2 secs

# Load Gene Ontology database
# use gene 'SYMBOL', or 'ENSEMBL' id
# use get_MSigDB() to load MSigDB
library(zenith)
go.gs <- get_GeneOntology("CC", to = "SYMBOL")
#> 
#> 

# Run zenith gene set analysis on result of dreamlet
res_zenith <- zenith_gsa(res.dl, go.gs, "group_idstim", progressbar = FALSE)

# for each cell type select 3 genesets with largest t-statistic
# and 1 geneset with the lowest
# Grey boxes indicate the gene set could not be evaluted because
#    to few genes were represented
plotZenithResults(res_zenith, 3, 1)
#> Warning: Removed 6 rows containing missing values (`geom_text()`).