Quantify expression with salmon
Usage
salmon_quantify(
sample_info = NULL,
filtdir = "results/03_filtered_FASTQ",
salmonindex = "results/05_quantification/salmon/idx",
salmondir = "results/05_quantification/salmon",
threads = NULL
)
Arguments
- sample_info
Data frame of sample metadata created with the functions
create_sample_info
andinfer_strandedness
. The functioninfer_strandedness
adds a column named "Orientation" with library strandedness information. If this column is not present in sample_info, salmon will automatically infer the library strandedness, but it will take longer to run.- filtdir
Path to the directory where filtered reads are stored. Default: results/03_filtered_FASTQ.
- salmonindex
Directory where the transcriptome index is stored. Default: results/05_quantification/salmon/idx.
- salmondir
Directory where quantification files will be stored. Default: results/05_quantification/salmon.
- threads
Number of threads for salmon quant.
Value
A 2-column data frame with BioSample IDs in the first column and salmon quantification status in the second column, with "OK" if salmon sucessfully quantified expression for a given BioSample, and NA otherwise.
Examples
data(sample_info)
filtdir <- system.file("extdata", package = "bears")
salmonindex <- tempdir()
salmondir <- tempdir()
transcriptome_path <- system.file(
"extdata", "Hsapiens_GRCh37.75_subset_transcripts.fa", package="bears"
)
if(salmon_is_installed()) {
salmon_index(salmonindex, transcriptome_path)
salmon_quantify(sample_info, filtdir, salmonindex, salmondir)
}