pp_hashtagDemultiplex: render rmarkdown file for de-multiplex hash-tag data of...

In zzwch/convgene: This package is designed to conveniently convert gene between human and mouse.

Description

render rmarkdown file for de-multiplex hash-tag data of h5file generated by cellranger

Usage

pp_hashtagDemultiplex(
  h5file,
  seuratfile,
  sample,
  hashtag = stringr::str_glue("B025{1:6}_anti-human_Hashtag_{1:6}"),
  output_format = "html_document",
  output_file = NULL,
  output_dir = "./"
)

Arguments

h5file	.h5 file generated by cellranger
seuratfile	save seurat obejct into this file, eg. 'hashtag.seurat.Rdata'
sample	real sample names represented by hash-tag, must be corresponding to hashtag each by each.
hashtag	hash-tag names used in the feature-ref file of your cellranger pipeline
output_format	The R Markdown output format to convert to. The option "all" will render all formats defined within the file. The option can be the name of a format (e.g. "html_document") and that will render the document to that single format. One can also use a vector of format names to render to multiple formats. Alternatively, you can pass an output format object (e.g. html_document()). If using NULL then the output format is the first one defined in the YAML frontmatter in the input file (this defaults to HTML if no format is specified there).
output_file	The name of the output file. If using NULL then the output filename will be based on filename for the input file. If a filename is provided, a path to the output file can also be provided. Note that the output_dir option allows for specifying the output file path as well, however, if also specifying the path, the directory must exist. If output_file is specified but does not have a file extension, an extension will be automatically added according to the output format. To avoid the automatic file extension, put the output_file value in I(), e.g., I('my-output').
output_dir	The output directory for the rendered output_file. This allows for a choice of an alternate directory to which the output file should be written (the default output directory of that of the input file). If a path is provided with a filename in output_file the directory specified here will take precedence. Please note that any directory path provided will create any necessary directories if they do not exist.

Details

Given that this package is designed for human, mouse and macaca, when Mitochondria genes did not start with "mt-" (case was ignored. This situation should only occur in Macaca), Ensembl gene id (already stored in this package) of Macaca mulatta will be used.

Value

derived html file

See Also

rmarkdown::render

zzwch/convgene documentation built on July 11, 2021, 9:41 a.m.