Parsing through snp matrix
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@genomic_region-13050
Last seen 3.1 years ago

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.

snpmatrix GGI • 487 views
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