format_david: Format DAVID output

Description

Format DAVID 'functional annotation and clustering' output to use with FGNet.

Usage

format_david(fileName, jobName = NULL, geneLabels = NULL, moveFile = FALSE, downloadFile=TRUE)

Arguments

fileName

character. URL or local file with the results of a DAVID analysis, for example, performed at DAVID's Website (http://david.abcc.ncifcrf.gov/summary.jsp). In case of local file, it should be the absolute path to the .txt file (whole location from root to the file including file name: "C:\\Documents\\23424203.txt", "/home/user/2342342.txt").

jobName

character. Folder name and prefix for the formatted files.

geneLabels

named character vector. Gene name or label to use in the report/plots instead of the original gene ID. The vector names should be the gene ID and the content of the vector the gene label. The resulting geneTermSets table will contain the original gene ID column (geneIDs) and the label column (Genes).

moveFile

logical. If TRUE the original file is moved to the new location. If FALSE, the file is copied.

downloadFile

logical. If TRUE, the result files are saved in the current directory (required to generate report).

Value

List. Same as fea_david.

References

[1] Huang DW, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37(1):1-13.

Examples

Run this code


# Select file:
txtFile <- "http://david.abcc.ncifcrf.gov/data/download/901234901248.txt"
txtFile <- paste(file.path(system.file('examples', package='FGNet')), 
    "DAVID_Yeast_raw.txt", sep="/")

# Read:
results <- format_david(txtFile, jobName="DavidAnalysis")


# To continue the workflow... (see help for further details)
getTerms(results)
incidMat <- fea2incidMat(results)
functionalNetwork(incidMat)

?FGNet_report