create_processed_report: create_processed_report

In scPipe: pipeline for single cell RNA-seq data analysis

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. (i.e '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.

Examples

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

## End(Not run)

scPipe documentation built on Nov. 8, 2020, 8:28 p.m.