#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)
}
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