Center view-data — center_views • MOFAcellulaR

Centers each element of a list of SummarizedExperiments

Usage

center_views(pb_dat_list)

Arguments

pb_dat_list: List of SummarizedExperiment generated from MOFAcellulaR::filt_profiles()

Value

A named list of SummarizedExperiments per cell type provided with centered pseudobulk profiles

Details

Given that the MOFA model in general uses centered data, when interested in projecting new data to a new manifold, it is needed to perform centering.

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)

ct_list <- center_views(pb_dat_list = ct_list)

multiview_dat <- pb_dat2MOFA(pb_dat_list = ct_list)