affyConvert: Affymetrix Convert
In mbertalan/iPsychCNV: iPsychCNV

Description Usage Arguments Details Value Author(s) Source Examples

Affymetrix Convert: Calculate LRR and BAF from Affymetix CEL files to allow for CNV detection with iPsych CNV.

1	affyConvert(PathToCel, Outdir = "affyConvert", PathToPennCNV, AffyAssay)

`PathToCel:`	The path to per sample Affymetrix CEL files.
`Outdir:`	Output directory for the processed data and conversion files.
`AffyAssay:`	Character string defining the affymetix assay to be converted (Affy_6.0 or Affy_5.0).

Compatable with conversion from Affymetrix Assay_6.0 and Assay_5.0. This function applies the instructions given for conversion of Affymetrix data to allow for PennCNV detection from http://penncnv.openbioinformatics.org/en/latest/user-guide/affy/

Data frame with predicted CNVs.

Johan Hilge Thygesen

http://biopsych.dk/iPsychCNV

# Download Affy6.0 example data from hapmap and run analysis
system("mkdir -p affy6.0_example")
system("wget ftp://anonymous@ftp.ncbi.nlm.nih.gov/hapmap/raw_data/hapmap3_affy6.0/CHEAP.tgz")
system("tar xvzf CHEAP.tgz -C affy6.0_example")
affyConvert(PathToCel = "affy6.0_example", Outdir = "affyConvert", PathToPennCNV = "/home/mydir/penncnv/", AffyAssay = "Affy_6.0")

# Download Affy5.0 example data from ... and run analysis
system("mkdir -p affy5.0_example")
system("wget http://www.affymetrix.com/support/downloads/data/GW_SNP5_GCOS_CEL_1.zip")
system("unzip GW_SNP5_GCOS_CEL_1.zip -d affy5.0_example")
affyConvert(PathToCel = "affy5.0_example", Outdir = "affyConvert", PathToPennCNV = "/home/mydir/penncnv/", AffyAssay = "Affy_5.0")