PloPathway {PloGO2} | R Documentation |
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.
PloPathway(zipFile = "none", reference = "none", data.file.name = "none", datafile.ignore.cols = 1, filesPath = ".", aggregateFun="sum", logAb=FALSE,...)
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 |
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.
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" |
J. Wu
# 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)