Question: Software For Assessing Correlation Of Cnvs And Phenotype (I.E. Cnvwas)
0
gravatar for pmoney1
6.2 years ago by
pmoney180
pmoney180 wrote:

Hi,

I'm wondering what the best software is to do a CNVwas? I.e. a GWAS with CNV data instead of SNP data?

I have CNV data from Affy Genome-Wide Human SNP Array 6.0 that was preprocessed using the DNAcopy package in R and its in the following format

sampleName | chromosome | start | stop | numberOfProbes | log2CNV

Thanks!

gwas cnv • 1.5k views
ADD COMMENTlink modified 4.0 years ago by jglessnd20 • written 6.2 years ago by pmoney180
2
gravatar for Matt Shirley
6.2 years ago by
Matt Shirley9.0k
Cambridge, MA
Matt Shirley9.0k wrote:

Check out CNVineta. It's a straightforward R package, hasn't been updated in a while, but I did successfully use it with Affymetrix GW6 arrays in this publication. You'll need the CEL files for the arrays, though.

Also, I know PLINK has some common CNV functionality, but it looks unfinished.

Update: I also missed this one - CNVruler - it looks pretty capable.

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Matt Shirley9.0k
0
gravatar for jglessnd
4.0 years ago by
jglessnd20
United States
jglessnd20 wrote:

Try ParseCNV

ADD COMMENTlink written 4.0 years ago by jglessnd20
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