create_processed_report {scPipe} | R Documentation

## 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. (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)

[Package scPipe version 1.4.1 Index]