aGFF-class
(Package: ACME) :
Class for storing GFF-like data
The GFF format is quite versatile while remaining simple. This class simply stores the annotation associated with a set of GFF files from the same regions of the genome along with some information about the samples from which the data came and the data (from the "score" column of the GFF file) themselves.
This function is used to find the nearest refseq transcript(s) to a point in the genome specified. Note that it is limited to the refseq transcripts listed at genome.ucsc.edu, where this function goes for information.
findRegions
(Package: ACME) :
Find all regions in data above p-value threshold
After the ACME calculation, each probe is associated with a p-value of enrichment. However, one often wants the contiguous regions associated with runs of p-values above a given p-value threshold.
A GFF format file is a quite flexible format for storing genomic data. Nimblegen uses these format files as one format for making chip-chip data available. This function reads these files, one per experiment and creates a resulting aGFF-class object.
providing 
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