annotation2fasta: write probes in FASTA
In VladaMilch/pdProbeRemap: What the package does (short line)

Description Usage Arguments Details Value Author(s) Examples

Fasta files from a pd.annotation object

1 2	annotation2fasta(originalAnnotationDir, celFilePath = "InputFilePath", author, email, organism, species, outputDir, reverse = FALSE)

`originalAnnotationDir`	directory that contains annotation files: `".pgf"`, `".clf"`, `".probeset.csv"`, `".mps"` and `".mps"` files, if annotation is PGF-based; `".cdf"` – Chip Definition file, `".CEL"` – example CEL file, `"probe_tab"` – tabulated .txt probes file
`celFilePath`	path to CEL file, if not present in `originalAnnotationDir` and annotation is CDF-based
`author`	`character`, name of the annotation package author
`email`	`character` e-mail of the annotation package author (must contain "@")
`organism`	`character` (ex: "Human")
`species`	`character` (ex: "Homo Sapiens")
`outputDir`	path to user-spesified output directory
`reverse`	`logical`, if `reverse = TRUE`, probe sequences are written in reverse order (not reverse complementary)

Fasta files with pobe sequences generated from a parsed data object (probe sequences and ids from original annotation).

writes "FASTA" file in directory outpurDir/Probe_Sequences_Fasta/ (created the directory if needed)

Vladislava Milchevskaya milchv@gmail.com

dir1 = "/Users/milchevs/ownCloud/ProbeRemapSteps14/inst/extdata/mogene2_affyLibFiles_pgfBased/"
outDir = "/Users/milchevs/ownCloud/ProbeRemapSteps14/OutPutDir/"
dir.create(outDir)
annotation2fasta(originalAnnotationDir = dir1, 
                organism = "Mouse", species = "Mus musculus", 
                author = "Vladislava Milchevskaya",
                email = "milchv@gmail.com",
                outputDir = outDir, 
                reverse = FALSE)