Quantify Transcript Abundances (Bulk RNA-seq)

Alias for mpaqt_quant() for backwards compatibility.

mpaqt_quant_bulk(
  index,
  sr_counts,
  lr_counts = NULL,
  positional_bias = NULL,
  n_bins = 50L,
  prior = NULL,
  max_iter = 100L,
  tolerance = 1e-04,
  prior_start = 25L,
  convergence_start = 25L,
  verbose = TRUE
)

Arguments

index

An mpaqt_index object or path to index RDS file

sr_counts

An mpaqt_counts_sr object or path to short-read counts

lr_counts

An mpaqt_counts_lr object or path to long-read counts (optional)

positional_bias

Type of positional bias correction: NULL (none), "3p" (3' bias), or "5p" (5' bias). Default is NULL.

n_bins

Number of distance bins for bias correction (default: 50)

prior

Data frame with transcript_id column and covariate columns for mixed-effects prior integration (deprecated, use prior_model)

max_iter

Maximum number of EM iterations (default: 100)

tolerance

Convergence tolerance for log-likelihood change (default: 1e-4)

prior_start

Iteration to start using prior information (default: 25)

convergence_start

Iteration to start checking convergence (default: 25)

verbose

Print progress messages (default: TRUE)

Value

An mpaqt_quant_result object

See also

mpaqt_quant() for the main quantification function