TMM normalization of single cell data sets — tmm

Performs for a list of SummarizedExperiments, TMM normalization scaled by a factor specified by the user.

Usage

tmm_trns(pb_dat_list, scale_factor = 1e+06)

Arguments

pb_dat_list: List of SummarizedExperiment generated from MOFAcellulaR::filt_profiles()
scale_factor: Numeric. Scaled counts are multiplied by this factor before log transformation

Value

A named list of SummarizedExperiments per cell type provided with normalized log transformed data in their logcounts assay

Details

This function estimates TMM normalization factors and normalizes a list of gene count matrices, data is additionally scaled using a factor specified by the user and log1p() transformed

Examples

inputs_dir <- base::system.file("extdata", package = "MOFAcellulaR")
load(file.path(inputs_dir, "testpbcounts.rda"))
load(file.path(inputs_dir, "testcoldata.rda"))

pb_obj <- create_init_exp(counts = testpbcounts,
                          coldata = testcoldata)

ct_list <- filt_profiles(pb_dat = pb_obj,
                         cts = c("Fib","CM"),
                         ncells = 5,
                         counts_col = "cell_counts",
                         ct_col = "cell_type")

ct_list <- filt_gex_byexpr(pb_dat_list = ct_list,
                           min.count = 5,
                           min.prop = 0.25)
#> Warning: All samples appear to belong to the same group.
#> Warning: All samples appear to belong to the same group.

ct_list <- tmm_trns(pb_dat_list = ct_list,
                    scale_factor = 1000000)