R - snpmatrix - data filtering

Question

[Bioinformatics_NewComer]

Hi all,

I'm interested to use genegeneinteraction R package. For that data are read and a snp matrix is generated. When I try to run gene gene interaction I get error

 GGI.res <- GGI(Y=Y, snpX=data$snpX, genes.info=data$genes.info,method="PCA")

Error:

Error in GGI(Y = Y, snpX = data$snpX, genes.info = data$genes.info, method = "PCA") : The snpMatrix must be complete. No NAs are allowed.

I am unable to get my way through this (snp matrix) data structure.

https://bioconductor.statistik.tu-dortmund.de/packages/2.8/bioc/manuals/snpMatrix/man/snpMatrix.pdf

Can anyone help in order to use signature function:

temp<-data$snpX [signature(x="temp",drop="missing")]  
 signature(x="temp",drop="missing")  
 []signature(x="temp",drop="missing")

http://www.imsbio.co.jp/RGM/R_rdfile?f=snpStats/man/SnpMatrix-class.Rd&d=R_BC

Also, I'm interested to view contents of it, but unable to print or subset them in readable manner.
Thanks.

[Ram]

You should post this on https://support.bioconductor.org. Also, use GGI and snpMatrix as tags so they pop up to people looking to answer questions on those topics.