Creating a GenomicRatioSet with non minfi normalized data
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hrishi27n ▴ 20
@hrishi27n-11821
Last seen 3 months ago
United States

I have methylation data that is pre-processed and normalized with an unpublished normalization method, I am hoping to run DMR and DMP analysis on this dataset using minfi.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. 

Code:

library(minfi)

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))

pdata <-read.table("MaleTargets.csv",header=TRUE,sep=",")

ratio <-GenomicRatioSet(Beta = Beta, M=Mval, pData=pdata)

print(ratio)

Error

Error in `rownames<-`(`*tmp*`, value = c("X10261170275986964480", "X10333227870024892416",  : 

  invalid rownames length

Calls: GenomicRatioSet ... SummarizedExperiment -> .local -> rownames<- -> rownames<-

Execution halted

 

minfi methylation illumina450k • 549 views
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