Error in if (max(sapply(1:J, function(x)

[Former user]

I am trying to run block.pls using three input datasets. There is pre and post methylation data (continuous values from 0 to 1) and SNP data (0,1,2 allele counts). The outcome is a continuous value. It runs when only having the methylation datasets as input. However when I add the SNP data I get the error:

Error in if (max(sapply(1:J, function(x) { : missing value where TRUE/FALSE needed

Any ideas?

[Kim-Anh Le Cao]

Hello, we do not deal with SNP data in mixOmics at the moment (we are currently developing an appropriate multivariate method for that specific purpose). The current model considers the SNP data as additive (numerical variable). The error probably comes from SNPs with null variance. You could try filter out some SNP using the function nearZeroVar, and be aware of the current limitations of block.pls in your interpretation. Hope that helps,

Kim-Anh

[sallyrose0425]

I got it working with that. Thanks!