create_processed_report: create_processed_report

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

create_processed_report

Description

Create an HTML report summarising pro-processed data. This is an alternative to the more verbose create_report that requires only the processed counts and stats folders.

Usage

create_processed_report(
  outdir = ".",
  organism,
  gene_id_type,
  report_name = "report"
)

Arguments

outdir	output folder.
organism	the organism of the data. List of possible names can be retrieved using the function 'listDatasets'from 'biomaRt' package. (e.g. 'mmusculus_gene_ensembl' or 'hsapiens_gene_ensembl').
gene_id_type	gene id type of the data A possible list of ids can be retrieved using the function 'listAttributes' from 'biomaRt' package. the commonly used id types are 'external_gene_name', 'ensembl_gene_id' or 'entrezgene'.
report_name	the name of the report .Rmd and .html files.

Value

file path of the created compiled document.

Examples

## Not run: 
create_report(
       outdir="output_dir_of_scPipe",
       organism="mmusculus_gene_ensembl",
       gene_id_type="ensembl_gene_id")

## End(Not run)

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.