PloPathway: Function to do steps of pathway annotation and...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/PloPathway.R

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

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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

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# 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)

PloGO2 documentation built on Nov. 8, 2020, 5:40 p.m.