TAGGITontology: TAGGITontology

In bakuhatsu/microarrayTools: Tools for microarray data analysis

TAGGITontology

Description

Original TAGGIT paper: (Carrera et al., 2007) This function is hardcoded for use with Arabidopsis ATH1 microarray data To use with data from another organism, you will need make a few edits.

Usage

TAGGITontology(geneList, useSearchTerms = TRUE,
  outputFileName = "TAGGITontologyHits.xlsx", annotationFile = "default",
  taggitAGIs = "default", taggitSearchTerms = "default")

Arguments

geneList	A vector of genes as AGI identiers or Affymetrix probe_ids.
useSearchTerms	Set to FALSE to prevent search term searches in gene descriptions (faster, but results will be based only on genes specified in taggitAGIs file)
outputFileName	Path to output excel file containing lists of hits with descriptions. File is output into the current working directory as "TAGGITontologyHits.xlsx" by default. Set to "none" for no output.
annotationFile	Use default unless you wish to provide your own updated myAnnot file. See description for instructions for creating this file.
taggitAGIs	Generally use default. Can also pass the path of your own taggitAGIs.tsv (tab-separated) file defining specific AGI identifiers for each TAGGIT term.
taggitSearchTerms	Generally use default. Can also pass the path of your own taggitSearchTerms.tsv (tab-separated) file defining TAGGIT term-specific search terms to search for within gene descriptions.

Value

A dataframe containing lists of hits for each TAGGIT term. Also can save an excel spreadsheet containing these hits with descriptions separated by TAGGIT term.

Examples

# Example data is provided, use the following code to load it
data("GeneSetdata") # loads GeneSet_UP and GeneSet_DOWN objects which contain example data.

## Make a list containing two vectors: 1) up-regulated genes, and 2) down-regulated gene
GeneSet <- list()
GeneSet$UP <- GeneSet_UP # A vector of upregulated genes
GeneSet$DN <- GeneSet_DOWN # A vector of down-regulated genes

## Create TAGGITontology objects
# (may take a few minutes, but the built-in progress bar will keep you informed on the progress)
# Returns dataframe for plotting and outputs an excel sheet of hits to the working directory.
GeneSet_TAGGIT_UP <- TAGGITontology(GeneSet$UP, outputFileName = "TAGGITontologyHits_UP.xlsx")
GeneSet_TAGGIT_DN <- TAGGITontology(GeneSet$DN, outputFileName = "TAGGITontologyHits_DN.xlsx")

## Plot the results of the TAGGIT analysis using ggplot2 via the TAGGITplot function
# Comparing UP and DOWN regulated genesets
TAGGITplot(GeneSet$UP, GeneSet$DN, GeneSet_TAGGIT_UP, GeneSet_TAGGIT_DN, title = "")
## Export the image: for best results export in EPS (vector) format
## For output like Figure 4 in the publication, export at 400x511 resolution

bakuhatsu/microarrayTools documentation built on March 26, 2024, 8:53 p.m.