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Build a charging count matrix for differential charging analysis.

Source: R/deseq.R
charging_count_matrix.Rd

Create a count matrix with two columns per sample (charged and uncharged), suitable for a DESeq2 interaction design that tests for differences in charging ratios between conditions.

Usage

charging_count_matrix(charging_data, min_count = 10)

Arguments

charging_data

A tibble of combined charging data with columns ref, counts_charged, counts_uncharged, and sample_id (as returned by read_charging_multi()).

min_count

Minimum total count across all columns for a tRNA to be retained. Default 10.

Value

An integer matrix with tRNA names as row names. Column names are {sample_id}_charged and {sample_id}_uncharged.

Examples

if (FALSE) { # \dontrun{
charging <- read_charging_multi(paths)
mat <- charging_count_matrix(charging)
} # }