pipeline: Pipeline

Description Usage Arguments Details Value

View source: R/47_pipeline.R

Description

TBA

Usage

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pipeline(sample_sheet, base_dir, ref_sample_sheet, ref_base_dir, report_dir,
  verbose = TRUE, cnv_sample_labels = list(query = "query", ref = "ref"))

Arguments

sample_sheet

A character scalar of query sample sheet file path. See read_sample_sheet() for sample sheet format.

base_dir

A character scalar of query base directory.

ref_sample_sheet

A character scalar of reference sample sheet file path. See read_sample_sheet() for sample sheet format.

ref_base_dir

A character scalar of reference base directory. if missing, it is set to base_dir argument.

report_dir

A character scalar of report directory path.

verbose

A logical scalar. Default to TRUE.

cnv_sample_labels

A list of two items, query and ref which label query and reference samples on the CNV_Sample_Label column respectively. Default is list(query="query", ref="ref").

Details

TBA

Value

A list of two MAAP objects (invisible), corresponding to query samples and reference samples respectively.


markgene/sjmat documentation built on April 26, 2018, 4:13 p.m.