affyConvert: Affymetrix Convert

Description Usage Arguments Details Value Author(s) Source Examples

View source: R/Affy_convert.R

Description

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

Usage

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

Arguments

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).

Details

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/

Value

Data frame with predicted CNVs.

Author(s)

Johan Hilge Thygesen

Source

http://biopsych.dk/iPsychCNV

Examples

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# Download Affy6.0 example data from hapmap and run analysis
system("mkdir -p affy6.0_example")
system("wget ftp://[email protected]/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")

mbertalan/iPsychCNV documentation built on June 30, 2017, 2:02 a.m.