#!/usr/bin/Rscript
"usage: performDE.R [options]
options:
--bamfiles=<file> bamfiles
--design=<file> design data frame
--gtffile=<file> gene feature file
--format=<string> pdf or html. [default: html]
" -> doc
library("docopt")
opts <- docopt(doc)
.design <- opts$design
if (is.null(.design)) {
.design <- system.file("extdata/sample_table.csv", package = "airway")
}
.bamfiles <- opts$bamfiles
if (is.null(.bamfiles)) {
.bamfiles <- list.files(system.file("extdata", package = "airway"), "*.bam",
full.names = TRUE
)
} else {
.bamfiles <- strsplit(opts$bamfiles, ",")[[1]]
}
.gtffile <- opts$gtffile
if (is.null(.gtffile)) {
.gtffile <- system.file("extdata/Homo_sapiens.GRCh37.75_subset.gtf",
package = "airway"
)
}
# create param list
lst <- list(
design = normalizePath(.design),
gtffile = normalizePath(.gtffile),
bamfiles = normalizePath(.bamfiles),
currentPath = normalizePath(".")
)
# render the report
.format <- switch(opts$format,
"pdf" = "pdf_document",
"html" = "html_document", {
"pdf_document"
}
)
rmarkdown::render("/report/rnaseqGene.Rmd", .format,
output_dir = ".",
params = lst
)
# For rabix execution in the cloud,
# this is now a workaround to move intermediate files
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