Hi All,
I'm keen to use genegeneinteractionR 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/Rrdfile?f=snpStats/man/SnpMatrix-class.Rd&d=RBC
Also, I'm interested to view contents of it, but unable to print or subset them in readable manner. Thanks.
PS: I posted this on biostars. They asked me to put it up on bioconductor.