knitr::opts_chunk$set(echo = TRUE, cache = FALSE, warning = FALSE, message = FALSE) library(tidyverse); library(knitr); library(GEOquery);
g <- getGEO("GSE147507") names(g) e1 <- g[["GSE147507_series_matrix.txt.gz"]] ## assay characteristics phenoData <- pData(e1) dim(phenoData) rownames(phenoData) <- make.names(sapply(strsplit(as.character(phenoData$description), "_"), function(i){i[[1]]})) ## transcriptomics mrna <- as.matrix(read.csv(here::here("inst", "extdata", "covid19", "GSE147507_RawReadCounts.tsv"), row.names = 1, sep = "\t")) colnames(mrna) <- gsub("_", ".", colnames(mrna)) ## check if both datasets are in the same order all(rownames(phenoData) == colnames(mrna)) demo <- setNames(phenoData[, c("cell type:ch1", "time point:ch1", "treatment:ch1")], c("cell", "time", "treatment")) %>% mutate(group = paste(time, treatment, sep="_"))
nrow(mrna);
mrna <- mrna[apply(mrna, 1, sd) !=0, ] mrna[mrna < 6] <- NA mrna <- t(na.omit(mrna)) dim(mrna);
## save covid19 datasets covid19 <- list( demo = demo, mrna = mrna ) usethis::use_data(covid19, overwrite = TRUE)
sessionInfo()
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