Transcript quantification — quantify

Calculate the transcript count matrix by parsing the re-alignment file.

Usage

quantify_transcript(
  annotation,
  outdir,
  config,
  pipeline = "sc_single_sample",
  ...
)

Arguments

annotation: The file path to the annotation file in GFF3 format
outdir: The path to directory to store all output files.
config: Parsed FLAMES configurations.
pipeline: The pipeline type as a character string, either sc_single_sample (single-cell, single-sample),
...: Supply sample names as character vector (e.g. samples = c("name1", "name2", ...)) for muti-sample or bulk pipeline. bulk (bulk, single or multi-sample), or sc_multi_sample (single-cell, multiple samples)

Value

A SingleCellExperiment object for single-cell pipeline, a list of SingleCellExperiment objects for multi-sample pipeline, or a SummarizedExperiment object for bulk pipeline.