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

In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

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)

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