kallisto_quantify: Quantify expression with kallisto

In almeidasilvaf/gead: Building Expression Atlas from RNA-Seq data

Quantify expression with kallisto

Description

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 and infer_strandedness. The function infer_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
    )
}

almeidasilvaf/gead documentation built on April 26, 2023, 3:47 p.m.