generate_report: From a ChromSCape analysis directory, generate an HTML...

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

From a ChromSCape analysis directory, generate an HTML report.

Description

From a ChromSCape analysis directory, generate an HTML report.

Usage

generate_report(
  ChromSCape_directory,
  prefix = NULL,
  run = c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage", "DA", "GSA",
    "report")[c(1, 3, 6, 7, 8, 9)],
  genes_to_plot = c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b", "Cdkn2a",
    "chr7:15000000-20000000"),
  control_samples_CNA = NULL
)

Arguments

ChromSCape_directory	Path towards the ChromSCape directory of which you want to create the report. The report will be created at the root of this directory.
prefix	Name of the analysis with the filtering parameters (e.g. Analysis_3000_100000_99_uncorrected). You will find the prefix in the Filtering_Normalize_Reduce subfolder.
run	Which steps to report ("filter", "CNA","cluster", "consensus", "peak_call", "coverage", "DA", "GSA", "report"). Only indicate steps that were done in the analysis. By default do not report CNA, consensus and peak calling.
genes_to_plot	For the UMAP, which genes do you want to see in the report.
control_samples_CNA	If running the Copy Number Alteration (CNA) part, which samples are the controls

Value

Generate an HTML report at the root of the analysis directory.

Examples

## Not run: 
generate_analysis("/path/to/data/", "Analysis_1")

## End(Not run)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.