levi {levi} | R Documentation

## levi

### Description

This is the Levi script mode. It allows you to create the integration of networks and gene expression levels as batch processing

### Usage

    levi(expressionInput, fileTypeInput, networkCoordinatesInput,
    networkInteractionsInput, geneSymbolnput, readExpColumn,
    contrastValueInput, zoomValueInput, resolutionValueInput,
    smoothValueInput, expressionLog, contourLevi, setcolor)

### Arguments

`expressionInput` | Filename of gene expression data, which is a numeric data.frame or matrix. The rows represent genes/proteins and the columns represent the experiment (RNA-seq, microarray, etc).
`fileTypeInput` | Filename of biological network. Levi can read files written in the following formats: Medusa (DAT), RedeR (DYN), Pajek (NET) and STRING/STITCH
`networkCoordinatesInput` | It allows the user to load the coordinate of the nodes the network.
`networkInteractionsInput` | Parameter available only to STRING/STITCH data format. It allows the user to load the interaction data file of the network.
`geneSymbolnput` | Column name from gene expression data containing the identifier (gene Symbol, Entrez ID, EMSEMBL, etc).
`readExpColumn` | Variable from readExpColumn function containing the comparisons of the experiments
`contrastValueInput` | Numeric value for image contrast. The variable range is 0 to 100. The default value is 50
`zoomValueInput` | Numeric value for image zoom. The variable range is 0 to 100. The default value is 50.
`resolutionValueInput` | Numeric value for image resolution. The variable range is 0 to 100. The default value is 50.
`smoothValueInput` | Numeric value for image smoothness. The variable range is 0 to 100. The default is 50.
`expressionLog` | Logical variable to indicate Log2 normalization in the expression levels. The default is FALSE
`contourLevi` | Logical variable to allow contour lines. The default is TRUE.
`setcolor` | Select the color palette to build the heatmat. The options available are: default, terrain, rainbow, heat, topo and cm.

### Details

Integrates the biological network and gene expression levels (or other type of data)

### Value

Return a image (heatmat).

### Author(s)

José Rafael Pilan (rafael.pilan@unesp.br)

### Examples

    template_network <- file.path(system.file(package="levi"),"extdata",
       "medusa.dat", fsep = .Platform$file.sep)
    template_expression <- file.path(system.file(package="levi"),
       "extdata","expression.dat", fsep = .Platform$file.sep)
    landscape <- levi(networkCoordinatesInput = template_network,
       expressionInput = template_expression, fileTypeInput = "dat",
       geneSymbolnput = "ID",
       readExpColumn=readExpColumn("TumorCurrentSmoker-NormalNeverSmoker"),
       contrastValueInput = 50, resolutionValueInput  = 50, zoomValueInput = 50,
       smoothValueInput = 50, expressionLog = FALSE, contourLevi = TRUE,
       setcolor = "default")

[Package levi version 1.2.0 Index]