I have methylation data that is pre-processed and normalized with an unpublished normalization method, I am hoping to run DMR and DMP analysis on this dataset using minfi. Currently, I have Beta values, M-values, P-values and pData(sample_info, age,sex etc), I am trying to create the GenomicRatioSet with the data that I have, the idea is that once I have the GenomicRatioSet class I could use minfi to run the further analysis. Does the GenomicRatioSet function also add the genomic co-ordinates? so far I have written the following: Is this the right way to do this? The execution of the following was stopped due to an error. Would really appreciate your help and guidance on this.
Beta <-as.matrix(read.csv("testGenomic.csv", header=T,sep=",", row.names=1))
Mval <- as.matrix(read.csv("testGenomicMVal.csv", header=T,sep=",", row.names=1))
ratio <-GenomicRatioSet(Beta = Beta, M=Mval, pData=pdata)
Error in `rownames<-`(`*tmp*`, value = c("X10261170275986964480", "X10333227870024892416", :
invalid rownames length
Calls: GenomicRatioSet ... SummarizedExperiment -> .local -> rownames<- -> rownames<-