FluteRRA {MAGeCKFlute}R Documentation

Downstream analysis based on MAGeCK-RRA result

Description

Integrative analysis pipeline using the gene summary table in MAGeCK RRA results

Usage

FluteRRA(gene_summary, prefix = "Test", enrich_kegg = "HGT",
  organism = "hsa", pvalueCutoff = 0.25, adjust = "BH", outdir = ".")

Arguments

gene_summary

A file path or a data frame, which has three columns named 'id', 'neg.fdr' and 'pos.fdr'.

prefix

A character, indicating the prefix of output file name.

enrich_kegg

One of "HGT"(HyperGemetric test), "ORT"(Over-Representing Test), "DAVID" and "GOstats", specifying enrichment method used for kegg enrichment analysis.

organism

A character, specifying organism, such as "hsa" or "Human"(default), and "mmu" or "Mouse"

pvalueCutoff

A numeric, specifying pvalue cutoff of enrichment analysis, default 1.

adjust

One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

outdir

Output directory on disk

Details

MAGeCK RRA allows for the comparison between two experimental conditions. It can identify genes and sgRNAs are significantly selected between the two conditions. The most important output of MAGeCK RRA is the file 'gene_summary.txt'. MAGeCK RRA will output both the negative score and positive score for each gene. A smaller score indicates higher gene importance. MAGeCK RRA will also output the statistical value for the scores of each gene. Genes that are significantly positively and negatively selected can be identified based on the p-value or FDR.

The downstream analysis of this function includes identifying positive and negative selection genes, and performing biological functional category analysis and pathway enrichment analysis of these genes.

Value

All of the pipeline results is output into the out.dir/prefix_Results, which includes a pdf file and a folder named 'RRA'.

Author(s)

Wubing Zhang

See Also

FluteMLE

Examples

data(RRA_Data)
gene_summary = RRA_Data
## Not run: 
    # Run the FluteRRA pipeline
    FluteRRA(gene_summary, prefix="BRAF", organism="hsa")

## End(Not run)



[Package MAGeCKFlute version 1.0.1 Index]