Create a SummarizedExperiment object from kallisto output

Usage

kallisto2se(
  sample_info = NULL,
  level = "gene",
  kallistodir = "results/05_quantification/kallisto",
  tx2gene = NULL,
  countsFromAbundance = "lengthScaledTPM"
)

Arguments

sample_info: Data frame of sample metadata created with the functions create_sample_info
level: Character indicating to which level expression must be quantified in the SE object. One of "gene" (default), "transcript", or "both". For "both", the SE object will have two assays named "transcript" and "gene".
kallistodir: Directory where quantification files will be stored. Default: results/05_quantification/kallisto.
tx2gene: Data frame of correspondence between genes and transcripts, with gene IDs in the first column and transcript IDs in the second column. Only required if level = 'gene' or 'both'.
countsFromAbundance: Exactly as in tximport::tximport, whether ot not to generate estimated counts using abundance estimates. One of "lengthScaledTPM" (default), "scaledTPM", "no", or "dtuScaledTPM". See ?tximport for details.

Value

A SummarizedExperiment object with gene/transcript expression levels and sample metadata.

Examples

data(sample_info)
data(tx2gene)
kallistodir <- system.file("extdata", package = "bears")
se_gene <- kallisto2se(sample_info, kallistodir = kallistodir, 
                       tx2gene = tx2gene)
#> Note: importing `abundance.h5` is typically faster than `abundance.tsv`
#> reading in files with read.delim (install 'readr' package for speed up)
#> 1 
#> 
#> summarizing abundance
#> summarizing counts
#> summarizing length