Build column metadata for DESeq2.

Create a data.frame of sample metadata suitable for DESeq2::DESeqDataSetFromMatrix(). For charging count matrices, the charge_status factor is added automatically.

Usage

build_coldata(count_matrix, sample_info = NULL)

Arguments

count_matrix

A count matrix from abundance_count_matrix() or charging_count_matrix().

sample_info

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

Value

A data frame with row names matching colnames(count_matrix).

Examples

results <- read_pipeline_results(
  clover_example("ecoli/config.yaml"),
  types = "charging"
)
mat <- abundance_count_matrix(results$charging)
build_coldata(mat)
#>                 sample_id
#> 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