Nothing
test.runPipeline <- function() {
## get data
tp53Genome <- TP53Genome()
tp53GenomicFeatures <- TP53GenomicFeatures()
fastq1 <- getPackageFile("extdata/H1993_TP53_subset2500_1.fastq.gz", "HTSeqGenie")
fastq2 <- getPackageFile("extdata/H1993_TP53_subset2500_2.fastq.gz", "HTSeqGenie")
## run the pipeline
save_dir <- runPipeline(
## input
input_file=fastq1,
input_file2=fastq2,
paired_ends=TRUE,
quality_encoding="illumina1.8",
## output
save_dir="test",
prepend_str="test",
overwrite_save_dir="erase",
## aligner
path.gsnap_genomes=path(directory(tp53Genome)),
alignReads.genome=genome(tp53Genome),
alignReads.sam_id="test",
## gene model
path.genomic_features=dirname(tp53GenomicFeatures),
countGenomicFeatures.gfeatures=basename(tp53GenomicFeatures)
)
checkTrue(TRUE, "runPipeline() runs without errors")
}
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