Extract residuals from dreamletResult

Extract residuals from dreamletResult

Usage

# S4 method for dreamletResult
residuals(object, y, ..., type = c("response", "pearson"))

Arguments

object

dreamletResult object

y

dreamletProcessedData object

...

other arguments

type

compute either "response" residuals or "pearson" residuals.

Value

residuals from model fit

Details

"response" residuals are the typical residuals returned from lm(). "pearson" residuals divides each residual value by its estimated standard error. This requires specifying y

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...
#> 0.27 secs
#>   CD14+ Monocytes...
#> 0.38 secs
#>   CD4 T cells...
#> 0.3 secs
#>   CD8 T cells...
#> 0.17 secs
#>   FCGR3A+ Monocytes...
#> 0.37 secs

# Differential expression analysis within each assay,
# evaluated on the voom normalized data
res.dl <- dreamlet(res.proc, ~group_id)
#>   B cells...
#> 0.19 secs
#>   CD14+ Monocytes...
#> 0.27 secs
#>   CD4 T cells...
#> 0.23 secs
#>   CD8 T cells...
#> 0.13 secs
#>   FCGR3A+ Monocytes...
#> 0.28 secs

# extract typical residuals for each assay (i.e. cell type)
# Return list with entry for each assay with for retained samples and genes
resid.lst <- residuals(res.dl)

# Get Pearson residuals:
# typical residuals scaled by the standard deviation
residPearson.lst <- residuals(res.dl, res.proc, type = "pearson")