- Run `make'

### Gene array structure directories:
- Run genestruct.R function. Requires PGF file and CSV annotation file from Affymetrix. E.g.:
  > source("genestruct.R")
  > genestruct("~/Desktop/HuGene-1_0-st-v1.r3.analysis_libraryfile/HuGene-1_0-st-v1.r3.pgf",
    "~/Desktop/HuGene-1_0-st-v1.na26.hg18.transcript.csv/HuGene-1_0-st-v1.na26.hg18.transcript.csv",
    "../inst/structDirs/HuGene-1_0-st-v1")

### Exon array structure directories:
- Install Ensembl core + X:Map MySQL databases
- Adapt and then run the scripts in transcripthit.rb*. The first two scripts create transcript-level TSV files and geneIDs/geneTranscripts mappings files respectively. The third creates gene-level TSV files.
- Optionally filter duplicated probesets. E.g.:
  ./filterduplicates transcripthit-homo_sapiens_core_56_37a.tsv transcripthit-homo_sapiens_core_56_37a-nodups.tsv
- Run exonstruct on PGF file from Affymetrix and the transcript/gene-level tsv file from above. E.g.:
  ./exonstruct ~/Desktop/HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.pgf \
    transcripthit-homo_sapiens_50_36l.tsv \
    ../inst/structDirs/HuEx-1_0-st-v2
- For transcript-level analysis, copy geneIDs.txt and geneTranscripts.txt to the structure directories. E.g.:
  cp geneIDs-homo_sapiens_core_50_36l.txt ../inst/structDirs/HuEx-1_0-st-v2/geneIDs.txt
  cp geneTranscripts-homo_sapiens_core_50_36l.txt ../inst/structDirs/HuEx-1_0-st-v2/geneTranscripts.txt


### For convenience
./exonstruct ~/Desktop/HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.pgf transcripthit-homo_sapiens_core_56_37a-nodups.tsv ../inst/structDirs/HuEx-1_0-st-v2
./exonstruct ~/Desktop/HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.pgf genehit-homo_sapiens_core_56_37a-nodups.tsv ../inst/structDirs/HuEx-1_0-st-v2-gene
./exonstruct ~/Downloads/MoEx-1_0-st-v1.r2/MoEx-1_0-st-v1.r2.pgf transcripthit-mus_musculus_core_56_37i-nodups.tsv ../inst/structDirs/MoEx-1_0-st-v1
./exonstruct ~/Downloads/MoEx-1_0-st-v1.r2/MoEx-1_0-st-v1.r2.pgf genehit-mus_musculus_core_56_37i-nodups.tsv ../inst/structDirs/MoEx-1_0-st-v1-gene
./exonstruct ~/Downloads/RaEx-1_0-st-v1.r2/RaEx-1_0-st-v1.r2.pgf transcripthit-rattus_norvegicus_core_56_34x-nodups.tsv ../inst/structDirs/RaEx-1_0-st-v1
./exonstruct ~/Downloads/RaEx-1_0-st-v1.r2/RaEx-1_0-st-v1.r2.pgf genehit-rattus_norvegicus_core_56_34x-nodups.tsv ../inst/structDirs/RaEx-1_0-st-v1-gene

cp geneTranscripts-homo_sapiens_core_56_37a.txt ../inst/structDirs/HuEx-1_0-st-v2/geneTranscripts.txt 
cp geneIDs-homo_sapiens_core_56_37a.txt ../inst/structDirs/HuEx-1_0-st-v2/geneIDs.txt 
cp geneTranscripts-mus_musculus_core_56_37i.txt ../inst/structDirs/MoEx-1_0-st-v1/geneTranscripts.txt 
cp geneIDs-mus_musculus_core_56_37i.txt ../inst/structDirs/MoEx-1_0-st-v1/geneIDs.txt 
cp geneTranscripts-rattus_norvegicus_core_56_34x.txt ../inst/structDirs/RaEx-1_0-st-v1/geneTranscripts.txt
cp geneIDs-rattus_norvegicus_core_56_34x.txt ../inst/structDirs/RaEx-1_0-st-v1/geneIDs.txt
