ExcelToPloGO: Function to add GO annotation to an Excel spread sheet

Description Usage Arguments Value Author(s) Examples

View source: R/ExcelToPloGO.R

Description

Function to add GO annotation to an Excel spread sheet

Usage

1
(fname, colName = "Uniprot", termFile= NA, compareWithReference="none", data.file.name = "none", outFolder = "PloGO2Output")

Arguments

fname

Name of the Excel spread sheet to be annotated

colName

The name of the column containing the protein identifiers

termFile

The name of the file containing the GO categories

compareWithReference

The name of the tab that serves as basis for enrichement comparison.

data.file.name

Abundance data for PloGO if any

outFolder

The output files folder

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

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)

D.Pascovici

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
## Not run: 
# where sample files are stored
path <- system.file("files", package = "PloGO2")
termFile = paste(path, "GODefault.txt", sep="/")
xlfile <- paste(path, "ResultsWGCNA_Input4PloGO2.xlsx", sep="/")

res <- (xlfile, termFile=termFile, compareWithReference="AllData")



## End(Not run)

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