Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
0
0
Entering edit mode
Last seen 2.0 years ago

I have run predictedMeth() on filtered rrbs data. However, I want to pull out the methylation matrix where each row is a region and column is sample. The issue is that the rownames are numeric values rather than positions. I did pull out the coordinates from the predictedMeth object but I am not sure that the order match between the rows of the methylation matrix and coordinates. I want to confirm that they are in the same order and that I am referring each region to the right position on the genome. Below is the code I have used.

> betas <- as.matrix(methLevel(predictedMeth))
> betas[1:2,1:2]
A1       A2
1   1 0.97
2   1 0.98
> coordinates <- as.data.frame(predictedMeth@rowRanges)
> coordinates[1:2,]
seqnames   start     end width strand cluster.id
1     chr5 3020638 3020638     1      *     chr5_1
2     chr5 3020656 3020656     1      *     chr5_1

biseq R methylation • 207 views
0
Entering edit mode

Yes the order is the same.