inst/rawData/Mouse.gut.architecture.bulk_MGAB.R

In jasonserviss/sp.scRNAseqData: Data and processing functions for the CIMseq.data package

#run from package root
#source('inst/rawData/countsMgfp/Mouse.gut.architecture.R')

packages <- c("CIMseq.data", "EngeMetadata", "dplyr")
purrr::walk(packages, library, character.only = TRUE)
rm(packages)

MGAB <- function(upload = TRUE, save = TRUE) {
  projectName <- "Mouse.gut.architecture.bulk_MGAB"
  shortName <- "MGAB"
  cat(paste0('Processing ', projectName, '\n'))

  googledrive::drive_auth(oauth_token = "inst/extData/gd.rds")
  Meta <- getMetadata(projectName)
  if("Missing" %in% colnames(Meta)) {
    Meta <- Meta %>%
      filter(is.na(Missing) | Missing == FALSE) %>%
      select(-Missing)
  }

  countData <- getCountsData(projectName)

  #move genes to rownames
  countData <- moveGenesToRownames(countData)

  #extract ERCC
  ercc <- detectERCCreads(countData)
  CountsERCC <- countData[ercc, ]
  Counts <- countData[!ercc, ]

  #remove non-genes
  Counts <- Counts[!detectNonGenes(Counts), ]

  #filter counts
  data <- filterCountsData(
    Counts, CountsERCC, geneMinCount = 0, cellMinCount = 1e5, geneName = "Actb",
    quantileCut.hk = 0.01, quantileCut.ercc = 1
  )

  #add filtered column to Meta
  Meta <- dplyr::mutate(Meta, filtered = dplyr::if_else(
    sample %in% colnames(data[[1]]),
    FALSE, TRUE
  ))

  #check all count samples in meta and vice versa
  #c1 <- all(!Meta$sample %in% colnames(Counts))
  #c2 <- all(!colnames(data[[1]]) %in% Meta$sample)
  #if(c1 & c2) {
  #  stop("all counts data not present in meta data")
  #}

  #rename
  Counts <- data[[1]]
  CountsERCC <- data[[2]]

  #save .rda
  if(save) saveRDA(projectName, Counts, CountsERCC, Meta)

  #upload .txt
  if(upload) processedDataUpload(projectName, Counts, CountsERCC, Meta)
}