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Table of Top Genes from dreamlet fit

Source: R/dreamlet.R
topTable-methods.Rd

Extract a table of the top-ranked genes from a dreamlet fit.

Usage

# S4 method for dreamletResult
topTable(
  fit,
  coef = NULL,
  number = 10,
  genelist = NULL,
  adjust.method = "BH",
  sort.by = "P",
  resort.by = NULL,
  p.value = 1,
  lfc = 0,
  confint = FALSE
)

Arguments

fit

dreamletResult object

coef

coef

number

number

genelist

genelist

adjust.method

adjust.method

sort.by

sort.by

resort.by

resort.by

p.value

p.value

lfc

lfc

confint

confint

Value

data.frame storing hypothesis test for each gene and cell type

See also

limma::topTable(), variancePartition::topTable()

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...
#> 0.26 secs
#>   CD8 T cells...
#> 0.13 secs
#>   FCGR3A+ Monocytes...
#> 0.3 secs

# Differential expression analysis within each assay,
# evaluated on the voom normalized data
res.dl <- dreamlet(res.proc, ~group_id)
#>   B cells...
#> 0.17 secs
#>   CD14+ Monocytes...
#> 0.23 secs
#>   CD4 T cells...
#> 0.17 secs
#>   CD8 T cells...
#> 0.11 secs
#>   FCGR3A+ Monocytes...
#> 0.22 secs

# show coefficients estimated for each cell type
coefNames(res.dl)
#> [1] "(Intercept)"  "group_idstim"

# extract results using limma-style syntax
# combines all cell types together
# adj.P.Val gives study-wide FDR
topTable(res.dl, coef = "group_idstim", number = 3)
#> DataFrame with 3 rows and 9 columns
#>               assay          ID     logFC   AveExpr         t     P.Value
#>         <character> <character> <numeric> <numeric> <numeric>   <numeric>
#> 1           B cells       ISG15   6.17666   10.2306   19.1083 1.26348e-14
#> 2 FCGR3A+ Monocytes      CXCL10   5.27610   11.9149   27.3747 7.09630e-14
#> 3           B cells       ISG20   3.60083   11.5794   16.0129 3.92209e-13
#>     adj.P.Val         B     z.std
#>     <numeric> <numeric> <numeric>
#> 1 5.67431e-11   23.2102   19.1083
#> 2 1.59347e-10   22.0773   27.3747
#> 3 5.87136e-10   20.2656   16.0129