indvExp_ds_4K: Downsampled cells and genes Zeisel 2018 dataset for TEINH15,...

In neurogenomics/scFlowExamples: Provide example datsets to run scFlow

Description

See link: http://mousebrain.org/celltypes/

Usage

indvExp_ds_4K

Format

An object of class list of length 6.

Source

The code to prepare the .Rda file file is: # create a temporary directory td <- tempdir() # create the placeholder file tf <- tempfile(tmpdir = td, fileext = ".loom") # download into the placeholder file download.file("https://storage.googleapis.com/linnarsson-lab-loom/l5_all.loom", tf) # tf="~/l5_all.loom" unzip(tf) allExp <- prep_zeisel2018(path = tf) keptExp <- merge_zeisel_celltypes(allExp, useCells = c("TEINH15", "TEINH19", "MGL1", "MOL1")) indvExp <- split_celltypes_byIndv(keptExp, joinCells = c("TEINH15", "TEINH19"), nCases = 3, jointName = "TEINH") keptExp_ds <- downsample_cells(keptExp = keptExp, prop_cell = c(0.5,0.5,0.05,0.02)) indvExp_ds <- split_celltypes_byIndv(keptExp_ds, joinCells = c("TEINH15", "TEINH19"), nCases = 3, jointName = "TEINH") keptExp_ds_4K <- downsample_cells(keptExp = keptExp, prop_cell = c(0.5,0.5,0.05,0.02), n_top_genes = 4000) indvExp_ds_4K <- split_celltypes_byIndv(keptExp_ds_4K, joinCells = c("TEINH15", "TEINH19"), nCases = 3, jointName = "TEINH") # Save dataset so that it can be used easily usethis::use_data(indvExp_ds_4K, overwrite = TRUE)

neurogenomics/scFlowExamples documentation built on Dec. 22, 2021, 1:13 a.m.