as.dreamletResult: Convert list of regression fits to 'dreamletResult'

In GabrielHoffman/dreamlet: Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Convert list of regression fits to dreamletResult

Description

Convert list of regression fits to dreamletResult for downstream analysis

Usage

as.dreamletResult(fitList, df_details = NULL)

Arguments

fitList	list of regression fit with dream()
df_details	data.frame storing assay details

Details

Useful for combining multiple runs of dreamletCompareClusters() into a single dreamletResult for downstream analysis

Value

object of class dreamletResult

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
)

# first comparison
ct.pairs <- c("B cells", "CD14+ Monocytes")
fit <- dreamletCompareClusters(pb, ct.pairs, method = "fixed")

# second comparison
ct.pairs2 <- c("B cells", "CD8 T cells")
fit2 <- dreamletCompareClusters(pb, ct.pairs2, method = "fixed")

# Make a list storing each result with a meaningful name
fitList <- list()

id <- paste0("[", ct.pairs[1], "]_vs_[", ct.pairs[2], "]")
fitList[[id]] <- fit

id <- paste0("[", ct.pairs2[1], "]_vs_[", ct.pairs2[2], "]")
fitList[[id]] <- fit2

# create a dreamletResult form this list
res.compare <- as.dreamletResult(fitList)
res.compare

GabrielHoffman/dreamlet documentation built on May 20, 2024, 2:05 p.m.