Results from the univariate regressions performed using can be combined in a post-processing step to perform multivariate hypothesis testing. In this example, we fit on transcript-level counts and then perform multivariate hypothesis testing by combining transcripts at the gene-level. This is done with the function.
Read in transcript counts from the package.
library(readr)
library(tximport)
library(tximportData)
# specify directory
path <- system.file("extdata", package = "tximportData")
# read sample meta-data
samples <- read.table(file.path(path, "samples.txt"), header = TRUE)
samples.ext <- read.table(file.path(path, "samples_extended.txt"), header = TRUE, sep = "\t")
# read assignment of transcripts to genes
# remove genes on the PAR, since these are present twice
tx2gene <- read_csv(file.path(path, "tx2gene.gencode.v27.csv"))
tx2gene <- tx2gene[grep("PAR_Y", tx2gene$GENEID, invert = TRUE), ]
# read transcript-level quatifictions
files <- file.path(path, "salmon", samples$run, "quant.sf.gz")
txi <- tximport(files, type = "salmon", txOut = TRUE)
# Create metadata simulating two conditions
sampleTable <- data.frame(condition = factor(rep(c("A", "B"), each = 3)))
rownames(sampleTable) <- paste0("Sample", 1:6)Perform standard analysis at the transcript-level
library(variancePartition)
library(edgeR)
# Prepare transcript-level reads
dge <- DGEList(txi$counts)
design <- model.matrix(~condition, data = sampleTable)
isexpr <- filterByExpr(dge, design)
dge <- dge[isexpr, ]
dge <- calcNormFactors(dge)
# Estimate precision weights
vobj <- voomWithDreamWeights(dge, ~condition, sampleTable)
# Fit regression model one transcript at a time
fit <- dream(vobj, ~condition, sampleTable)
fit <- eBayes(fit)Combine the transcript-level results at the gene-level. The mapping between transcript and gene is stored in as a list.
# Prepare transcript to gene mapping
# keep only transcripts present in vobj
# then convert to list with key GENEID and values TXNAMEs
keep <- tx2gene$TXNAME %in% rownames(vobj)
tx2gene.lst <- unstack(tx2gene[keep, ])
# Run multivariate test on entries in each feature set
# Default method is "FE.empirical", but use "FE" here to reduce runtime
res <- mvTest(fit, vobj, tx2gene.lst, coef = "conditionB", method = "FE")
# truncate gene names since they have version numbers
# ENST00000498289.5 -> ENST00000498289
res$ID.short <- gsub("\\..+", "", res$ID)Perform gene set analysis using on the gene-level test statistics.
# must have zenith > v1.0.2
library(zenith)
library(GSEABase)
gs <- get_MSigDB("C1", to = "ENSEMBL")
df_gsa <- zenithPR_gsa(res$stat, res$ID.short, gs, inter.gene.cor = .05)
head(df_gsa)## NGenes Correlation delta se p.less p.greater PValue Direction
## chr7p13 28 0.05 7.144240 2.034359 0.999776828 0.0002231723 0.0004463445 Up
## chr11p13 32 0.05 -5.752953 1.982804 0.001859931 0.9981400686 0.0037198628 Down
## chr4p14 25 0.05 -5.077180 2.084132 0.007428521 0.9925714788 0.0148570424 Down
## chr2q37 75 0.05 3.571510 1.758652 0.978855126 0.0211448742 0.0422897483 Up
## chr2q36 21 0.05 -4.130558 2.168488 0.028411437 0.9715885626 0.0568228749 Down
## chr18q22 18 0.05 4.108195 2.252712 0.965889229 0.0341107714 0.0682215427 Up
## FDR Geneset coef
## chr7p13 0.1129252 chr7p13 zenithPR
## chr11p13 0.4705626 chr11p13 zenithPR
## chr4p14 0.9996791 chr4p14 zenithPR
## chr2q37 0.9996791 chr2q37 zenithPR
## chr2q36 0.9996791 chr2q36 zenithPR
## chr18q22 0.9996791 chr18q22 zenithPR## R version 4.5.1 (2025-06-13)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
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## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
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## attached base packages:
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## other attached packages:
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## [4] XML_3.99-0.18 AnnotationDbi_1.70.0 IRanges_2.42.0
## [7] S4Vectors_0.46.0 Biobase_2.68.0 BiocGenerics_0.54.0
## [10] generics_0.1.4 zenith_1.10.0 tximportData_1.36.0
## [13] tximport_1.36.1 readr_2.1.5 edgeR_4.6.3
## [16] pander_0.6.6 variancePartition_1.38.1 BiocParallel_1.42.1
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