make_sample_sheet: Make a sample sheet reflecting the samples apparent in...

In amcdavid/Genesee: Core functions for genomics project templating

Make a sample sheet reflecting the samples apparent in rawdata

Description

The sample sheet all_samples_files.csv maps between sequencing runs and other covariates.

Usage

make_sample_sheet(
  project_directory = NULL,
  write = TRUE,
  overwrite = FALSE,
  type = NULL
)

Arguments

project_directory	directory of the Genesee project. If set to NULL then will use working directory as long as a 'config.yml“ is present.
write	logical should the sample sheet be written to file, or just returned for further messaging
overwrite	logical should an existing sheet be overwritten?
type	character The type of project. One of scRNA and scVDJ. If set to NULL then will attempt to read from config.yml.

Details

At the moment, Cellranger mRNA (type = 'scRNA') and Cellranger VDJ (type = 'scVDJ') are supported.

Value

path of sample sheet (for additional editing) or sample sheet itself

amcdavid/Genesee documentation built on April 14, 2022, 5:16 a.m.