library(optparse)
## require rtracklayer package
option_list <- list(
make_option(c("--rawH5File"), type = "character"),
make_option(c("--outdir"), type = "character"),
make_option(c("--outfnm"), type = "character"),
make_option(c("--geneBedFile"), type = "character"),
make_option(c("--excludeChrs"), type = "character", default = "chrM", help = "string seperated by comma"),
make_option(c("--genome"), type = "character", default = "mm10"),
make_option(c("--barcodeFile"), type = "character", help = "no header, just one column of barcodes."),
make_option(c("--sampleName"), type = "character")
)
args <- parse_args(OptionParser(option_list = option_list))
message("Load gene bed files.")
genes <- rtracklayer::import(args$geneBedFile, format = "bed")
genenms <- genes$name
message("Load barcodes.")
barcodes <- read.table(file = args$barcodeFile, header = FALSE, comment.char = "")
barcodes <- barcodes$V1
excludeChr <- unlist(strsplit(args$excludeChr, split = ","))
message("Generate Gene Matrix.")
invisible(smmtools::getGeneMatrix(rawH5File = args$rawH5File,
outdir = args$outdir,
outfilenm = args$outfnm,
genes = genes, genenms = genenms,
genome = args$genome,
excludeChr = excludeChr,
sampleName = args$sampleName,
barcodes = barcodes
))
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