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Welcome

The package affy2sv contains a set of tools to extract the required files for analyzing different structural variants (CNVs, mosaicisms, inversions,...) from Affymetrix .CEL files (Genome Wide SNP 5.0/6.0, Axiom and CytoScan HD/750K). This is a collaboration between Carles Hernandez-Ferrer (CREAL) and Juan R. Gonzalez (CREAL).

The package affy2sv generates compatible output objects and files for MAD, invClust, snpStats, R-GADA, PLINK and PennCNV.

Disclaimers

  • The package affy2sv is under development/update.
  • The v 1.0.X version of the package is full supported under GNU/Linux and Windows systems and partially supported under MAC OS (it has not tested).

The package affy2sv is being developed and improved. Contact us, the developer and the maintainer, for any problem or question you may have about the package and the way to use it. But please, be patient since we will update the sources and the distributable file some times along the day.

Installation

The package affy2sv has several dependences, some are R packages others are external dependences.

To install the package we can download the lastest version from the Downloads and install it with:

install.packages("../downloads/affy2sv_1.0.X.tar.gz", type="source", repo=NULL)

Otherwise the first release affy2sv v0.99 can be installed using the CREAL installer in an R session:

source("http://www.creal.cat/media/upload/arxius/jr/CREAL_install/install.R")
creal.install("affy2sv")

Analysis

The following sections includes some code snippets in order to show how the package affy2sv can be used to process each accepted Affymetrix array anc reate input files for MAD, snpStats,...

DISCLAIMER: The sections will be completed during the upgrade.

Vignettes

DISCLAIMER: The sections will be completed during the upgrade.

Other Topics

Converting transposed format (TPED) to classic format (PED) with PLINK

Updated