PloPathway {PloGO2} | R Documentation

## Function to do steps of pathway annotation and annotation/abundance plots

### Description

Summarize pathway categories for all the files in the zip, if provided merge data from data file, generate annotation and abundance plots and comparison with reference.

### Usage

    PloPathway(zipFile = "none", reference = "none", data.file.name = "none", datafile.ignore.cols = 1, filesPath = ".", aggregateFun="sum", logAb=FALSE,...)

### Arguments

`zipFile` | Zip containing all the GO files
`reference` | The file name of the reference file, if any, for instance "Control" for Control.txt
`data.file.name` | The file containing all the experimental data, for instance "NASF.csv"
`datafile.ignore.cols` | The number of columns in the experimental file given in data.file.name that should not be used as numerical, for instance 2 if there is an ID field and a Description field. By default 1.
`filesPath` | If the zip file is not provided, the path to the GO files
`aggregateFun` | Either "sum" or "product"; the aggregation operation for abundance data
`logAb` | TRUE or FALSE; the abundance data to be logged or not
`...` | Parameters to pass

### Details

Process all the pathway files provided, in the directory or the zip, and assign ID's to the respective categories. If a reference is provided, then the numbers of identifiers in each category is compared to the reference by means of Fisher's exact test. If a data file is provided, then the quantitative values are aggregated into the sets.

### Value

A list object, with the following values:

`Counts` | The GO counts matrix summarized for all files
`Percentages` | The GO percentages matrix summarized for all files
`Abundance` | The GO percentages matrix summarized for all files, ONLY generated if an abundance file was provided
`aggregatedAbundance` | The aggregated abundance matrix if the data file is provided
`FisherPval` | The Fisher p-values matrix summarized for all files, ONLY generated if a reference file was provided
`res.list` | The full list result of processAnnotation function
`list.levelplots` | The abundance levelplots if the data.file.name is not "none"
`list.barplots` | The abundance barcharts if the data.file.name is not "none"

### Author(s)

J. Wu

### See Also

`processAnnotation`

### Examples

    # where sample files are stored
    path <- system.file("files", package = "PloGO2")
    # run PloPathway with list of id's, data file and reference
    res <- PloPathway( zipFile=paste(path, "PWFiles.zip", sep="/"),
    	reference="Alldata",
    	data.file.name = paste(path, "Abundance_data.csv", sep="/"),
    	datafile.ignore.cols = 1)

[Package PloGO2 version 1.6.0 Index]