FluteMLE {MAGeCKFlute} | R Documentation

## Downstream analysis based on MAGeCK-MLE result

### Description

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

### Usage

    FluteMLE(gene_summary, ctrlname, treatname, keytype = "Symbol",
      organism = "hsa", scale_cutoff = 1, top = 10, bottom = 10,
      interestGenes = NA, pathway_limit = c(3, 50), pvalueCutoff = 0.25,
      adjust = "BH", enrich_kegg = "HGT", gsea = FALSE,
      posControl = NULL, loess = FALSE, prefix = "", width = 10,
      height = 7, outdir = ".", view_allpath = FALSE)

### Arguments

`gene_summary` | Either a file path or a data frame, which contains columns of 'Gene', `ctrlname`.beta and `treatname`.beta which corresponding to the parameter ctrlname and treatmname.
`ctrlname` | A character vector, specifying the names of control samples.
`treatname` | A character vector, specifying the names of treatment samples.
`keytype` | Type of gene id in 'gene_summary', which should be one of "Entrez" or "Symbol".
`organism` | "hsa" or "mmu".
`scale_cutoff` | Boolean or numeric, whether scale cutoff to whole genome level, or how many standard deviation will be used as cutoff.
`top` | An integer, specifying number of top selected genes to be labeled in rank figure.
`bottom` | An integer, specifying number of bottom selected genes to be labeled in rank figure.
`interestGenes` | A character vector, specifying interested genes to be labeled in rank figure.
`pathway_limit` | A two-length vector (default: c(3, 50)), specifying the minimal and maximal size of gene sets for enrichent analysis.
`pvalueCutoff` | A numeric, specifying pvalue cutoff of enrichment analysis, default 1.
`adjust` | One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
`enrich_kegg` | One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test).
`gsea` | Boolean, indicating whether GSEA analysis is needed for positive and negative selection genes.
`posControl` | A file path or a character vector, specifying a list of gene entrezid as positive controls used for cell cycle normalization.
`loess` | Boolean, whether include loess normalization in the pipeline.
`prefix` | A character, indicating the prefix of output file name, which can't contain special characters.
`width` | The width of summary pdf in inches.
`height` | The height of summary pdf in inches.
`outdir` | Output directory on disk.
`view_allpath` | Boolean, whether output all pathway view figures.

### Details

MAGeCK-MLE can be used to analyze screen data from multi-conditioned experiments. MAGeCK-MLE also normalizes the data across multiple samples, making them comparable to each other. The most important ouput of MAGeCK MLE is 'gene_summary' file, which includes the beta scores of multiple conditions and the associated statistics. The 'beta score' for each gene describes how the gene is selected: a positive beta score indicates a positive selection, and a negative beta score indicates a negative selection.

The downstream analysis includes identifying essential, non-essential, and target-associated genes, and performing biological functional category analysis and pathway enrichment analysis of these genes. The function also visualizes genes in the context of pathways to benefit users exploring screening data.

### Value

All of the pipeline results is output into the `out.dir`/`prefix`_Results, which includes a pdf file and many folders. The pdf file 'prefix_Pipeline_results.pdf' is the summary of pipeline results. For each section in this pipeline, figures and useful data are outputed to corresponding subfolders. Distribution_of_BetaScores: Density plot and violin plot of beta scores. MAplot: Maplot for each normalized data. Linear_Fitting_of_BetaScores: Linear fitting of beta scores indicates the difference of cell cycle time between Control and Treatment samples. Scatter_Treat_Ctrl: Positive selection and negative selection Enrichment_Treat-Ctrl: Enrichment analysis for positive and negative selection genes Pathview_Treat_Ctrl: Pathway view for top enriched pathways Scatter_9Square: Using 9 Square to select drug related genes Enrichment_9Square: Enrichment analysis for selected genes Pathview_9Square: Pathway view for top enriched pathways

### Author(s)

Wubing Zhang

### See Also

`FluteRRA`

### Examples

    data(mle.gene_summary)
    ## Not run:
      # functional analysis for MAGeCK MLE results
      FluteMLE(mle.gene_summary, ctrlname = c("dmso"), treatname = c("plx"),
               prefix = "PLX", pvalueCutoff = 0.25, organism = "hsa")

    ## End(Not run)

[Package MAGeCKFlute version 1.2.3 Index]