## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- library(GEOfastq) ## ----eval = FALSE------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("GEOfastq") ## ----------------------------------------------------------------------------- gse_name <- 'GSE133758' gse_text <- crawl_gse(gse_name) ## ----------------------------------------------------------------------------- gsm_names <- extract_gsms(gse_text) gsm_name <- gsm_names[182] srp_meta <- crawl_gsms(gsm_name) ## ----------------------------------------------------------------------------- data_dir <- tempdir() # example using smaller file srp_meta <- data.frame( run = 'SRR014242', row.names = 'SRR014242', gsm_name = 'GSM315559', ebi_dir = get_dldir('SRR014242'), stringsAsFactors = FALSE) res <- get_fastqs(srp_meta, data_dir) ## ----echo=FALSE--------------------------------------------------------------- sessionInfo()