R/read_geo.R

In AllenInstitute/scrattch.io: scrattch File Input/Output Handling

#' Get data from GEO
# geo_to_list <- function(accession) {
#
#   all_packages <- installed.packages()[,"Package"]
#
#   if(!sum(c("GEOquery","Biobase") %in% all_packages) == 2) {
#
#     run_install <- readline(prompt="Install GEOquery and Biobase from Bioconductor? y/N: \n")
#
#     if(run_install == "y") {
#
#       install_GEO_deps()
#
#     } else {
#       stop("Required dependencies not installed. Exiting function.")
#     }
#   } else {
#
#     library(Biobase)
#     library(GEOquery)
#     library(dplyr)
#
#     cat("Retrieving data for",accession,"from GEO\n")
#
#     gset <- try(getGEO(accession, GSEMatrix = T), silent = T)
#
#     gset <- gset[[1]]
#
#     gpl <- annotation(gset)
#
#     cat("Retrieving platform annotations for",gpl,"from GEO\n")
#
#     platf <- getGEO(gpl, AnnotGPL=TRUE)
#     ncbifd <- data.frame(attr(dataTable(platf), "table"))
#
#     id_to_names <- ncbifd %>%
#       select(ID,Gene.symbol)
#     names(id_to_names) <- c("probe_id","gene")
#
#     ex <- as.data.frame(exprs(gset))
#
#
#     data <- ex %>%
#       mutate(probe_id = rownames(ex)) %>%
#       left_join(id_to_names) %>%
#       select(-probe_id) %>%
#       filter(gene != "") %>%
#       select(one_of(c("gene",names(ex)))) %>%
#       group_by(gene) %>%
#       filter(row_number() == 1) %>%
#       ungroup() %>%
#       mutate(gene = sub("///.+","",gene)) %>%
#       mutate(gene = sub("-",".",gene)) %>%
#       arrange(gene) %>%
#       as.data.frame()
#
#     row.names(data) <- 1:nrow(data)
#
#     samples <- names(ex)
#     genes <- data$gene
#
#     all.anno <- pData(gset)
#
#     list(data = data, anno = all.anno)
#
#   }
#
# }