Question: copy number variation as a covariate in MatrixEQTL
0
gravatar for mms140130
21 months ago by
mms14013060
mms14013060 wrote:

I want to add the copy number variation as a covariate in the model by MatrixEQTL, but I have 20,000 rows and 1069 columns, this won't work as the number rows is greater than the number of samples

How can I fix that?

snp R gene • 558 views
ADD COMMENTlink written 21 months ago by mms14013060
0
gravatar for Fabio Marroni
21 months ago by
Fabio Marroni2.1k
Italy
Fabio Marroni2.1k wrote:

I don't think that adding 20,000 covariates is a good idea. You should do a PCA analysis on the CNV data and then use the first X components (where X is a number between 2 and 10, let's say) as covariates. PCA can used to correct for population structure (doing PCA on the genotype data) or to incorporate unaccounted bias in genotypes (e.g. I also suggest that you use as a covariate the PCA of your expression data). There is lot of discussion on the use of PCA in GWAS. You will find useful references here.

ADD COMMENTlink written 21 months ago by Fabio Marroni2.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 755 users visited in the last hour