Create a SummarizedExperiment from pipeline output.

Read a pipeline configuration file and load all result types into a SummarizedExperiment::SummarizedExperiment object. The returned object contains count matrices as assays, tRNA metadata as rowData, and sample metadata as colData.

Usage

create_clover(
  config_path,
  types = c("charging", "bcerror", "odds_ratios"),
  sample_info = NULL,
  min_count = 10
)

Arguments

config_path

Path to a pipeline config.yaml file.

types

Character vector of result types to load. Valid values: "charging", "bcerror", "odds_ratios".

sample_info

An optional data frame with a sample_id column and additional experimental factor columns (e.g., condition, replicate). If NULL, a minimal colData is created from sample names.

min_count

Minimum total count across all samples for a tRNA to be retained in count matrices. Default 10.

Value

A SummarizedExperiment::SummarizedExperiment with:

• assay "counts": abundance count matrix (charged + uncharged)

• colData: sample metadata

• metadata: list with $config, $charging, $bcerror, $odds_ratios, $fasta as available

Examples

if (FALSE) { # \dontrun{
se <- create_clover("path/to/config.yaml")
SummarizedExperiment::assay(se, "counts")
SummarizedExperiment::colData(se)
} # }