## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----------------------------------------------------------------------------- suppressPackageStartupMessages({ library("waddR") library("SingleCellExperiment") library("BiocFileCache") }) ## ----------------------------------------------------------------------------- url.base <- "https://github.com/goncalves-lab/waddR-data/blob/master/data/" sce.blood.url <- paste0(url.base, "data_blood.rda?raw=true") sce.decidua.url <- paste0(url.base, "data_decidua.rda?raw=true") getCachedPath <- function(url, rname){ bfc <- BiocFileCache() # fire up cache res <- bfcquery(bfc, url, field="fpath", exact=TRUE) if (bfccount(res) == 0L) cachedFilePath <- bfcadd(bfc, rname=rname, fpath=url) else cachedFilePath <- bfcpath(bfc, res[["rid"]]) cachedFilePath } load(getCachedPath(sce.blood.url, "data_blood")) load(getCachedPath(sce.decidua.url, "data_decidua")) ## ----------------------------------------------------------------------------- set.seed(28) randgenes <- sample(rownames(data_blood), 1000, replace=FALSE) sce.blood <- data_blood[randgenes, ] sce.decidua <- data_decidua[randgenes, ] ## ----------------------------------------------------------------------------- assays(sce.blood) assays(sce.decidua) ## ----------------------------------------------------------------------------- res <- wasserstein.sc(sce.blood, sce.decidua, method="TS",permnum=1000,seed=24) head(res, n=10L) ## ----session-info------------------------------------------------------------- sessionInfo()