Quantify expression with kallisto
Usage
kallisto_quantify(
sample_info = NULL,
qc_table = NULL,
filtdir = "results/03_filtered_FASTQ",
kallistoindex = "results/05_quantification/kallisto/idx",
kallistodir = "results/05_quantification/kallisto",
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, which is mandatory for kallisto quantification.- qc_table
Data frame of fastp summary statistics as returned by
summary_stats_fastp()
.- filtdir
Path to the directory where filtered reads are stored. Default: results/03_filtered_FASTQ.
- kallistoindex
Directory where kallisto index file will be stored. Default: results/05_quantification/kallisto/idx.
- kallistodir
Directory where quantification files will be stored. Default: results/05_quantification/kallisto.
- threads
Number of threads for kallisto quant.
Value
A 2-column data frame with BioSample IDs in the first column and quantification status in the second column, with "OK" if kallisto successfully quantified expression for a given BioSample, and NA otherwise.
Examples
data(sample_info)
qc_table <- summary_stats_fastp(system.file("extdata", package = "bears"))
filtdir <- system.file("extdata", package = "bears")
kallistoindex <- file.path(tempdir(), "transcripts.idx")
kallistodir <- tempdir()
transcriptome_path <- system.file(
"extdata", "Hsapiens_GRCh37.75_subset_transcripts.fa", package="bears"
)
if(kallisto_is_installed()) {
kallisto_index(kallistoindex, transcriptome_path)
kallisto_quantify(
sample_info, qc_table, filtdir, kallistoindex, kallistodir
)
}