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Create a SummarizedExperiment from pipeline output.

Source: R/clover-se.R
create_clover.Rd

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

se <- create_clover(clover_example("ecoli/config.yaml"))
SummarizedExperiment::assay(se, "counts")[1:3, ]
#>                                 wt-15-ctl-01 wt-15-ctl-02 wt-15-ctl-03
#> host-tRNA-Ala-GGC-1-1                    298          397          113
#> host-tRNA-Ala-GGC-1-1-uncharged         4393         5014          883
#> host-tRNA-Ala-GGC-1-2                   1625         1506          265
#>                                 wt-15-inf-01 wt-15-inf-02 wt-15-inf-03
#> host-tRNA-Ala-GGC-1-1                    189          347         1253
#> host-tRNA-Ala-GGC-1-1-uncharged         3640         7133        12837
#> host-tRNA-Ala-GGC-1-2                   1299         1857         4409
SummarizedExperiment::colData(se)
#> DataFrame with 6 rows and 1 column
#>                 sample_id
#>               <character>
#> wt-15-ctl-01 wt-15-ctl-01
#> wt-15-ctl-02 wt-15-ctl-02
#> wt-15-ctl-03 wt-15-ctl-03
#> wt-15-inf-01 wt-15-inf-01
#> wt-15-inf-02 wt-15-inf-02
#> wt-15-inf-03 wt-15-inf-03