abundancePlot |
Function to summarize and plot abundance information from an annotations results list |
aggregateAbundance |
Function to aggregate the abundance by the group provided |
annotationPlot |
Function to summarize and plot extracted GO annotation |
Children |
Function to extract the children |
compareAnnot |
Function to compare annotation percentages |
countAndAbundance |
Function to do a side by side annotation and abundance plot |
Error |
Error |
extract.param |
Function to extract a parameter from the metatable |
extractPairs |
Extract annotation and abundance side by side for two files |
genWegoFile |
Function to generate a format in Wego native style from a list of Uniprot identifiers |
getGoID |
Function to map a vector of GO terms to the corresponding GO ID's |
GOGraphWrapper |
Simple wrapper for GOGraph |
GOParent |
Function to find the first parent of a GO node |
GOTermList |
Function to extract a list of GO terms at level 2,3 or 4 of the GO hierarchy |
inGraph |
Function to decide if a particular term is in a graph |
PloGO |
Function to do steps of GO annotation and annotation/abundance plots |
plotMat |
A levelplot of abundance by GO category |
processAnnotation |
Function to process a set of annotation files given a list of GO identifiers of interest |
processAnnotFile |
Function to process a single file in wego-like native format |
processGoFile |
Function to process a single file in wego-like native format |
processPlainAnnotation |
Function to process a set of annotation files given a list of identifiers of interest |
read.annot.file |
Function to read an annotation file. |
readMeta |
Utility function to process metafile |
writeAnnotation |
Function to print GO annotation to files |
writeGOannot |
Function to write annotation out to a file |