can you provide more details about data preparation?

[szcf-weiya]

Dear Lamian author,

I am interested in your wonderful work! Particularly, I want to follow your Covid data part, but I am not quite clear about your data pre-processing.

trajectory_variability/covid_data_analysis/Su_2020_Cell/data/01_preparedata.R

Lines 4 to 14 in 113aa75

	d <- readRDS('covid/Su_2020_Cell/data/CD8integrate.rds')
	data <- as.matrix(d@assays$RNA@data)
	order <- readRDS('covid/Su_2020_Cell/data/order.rds')
	data <- data[, order]
	saveRDS(data, 'covid/Su_2020_Cell/data/log2norm.rds')
	pt <- seq(1, length(order))
	names(pt) <- order
	saveRDS(pt, 'covid/Su_2020_Cell/data/tActivate_pseudotime.rds')
	meta <- readRDS('covid/Su_2020_Cell/data/meta.rds')

Specifically, how did you pre-process the data to get the CD8integrate.rds, order.rds, meta.rds?

Much appreciate if you could share the corresponding preprocessing code, or the saved rds files. Thanks.