dmrseq fails while processing chromosomes/contigs

[jckhearn]

Hi @kdkorthauer,

I am running dmrseq on WGBS of a sparsely methylated genome and it is failing with the following error:

Error in [[<-.data.frame(tmp, i, value = c(1L, 1L, 1L, 1L, 1L, 1L, : replacement has 480 rows, data has 240 Calls: dmrseq ... model.matrix -> model.matrix.default -> [[<- -> [[<-.data.frame

The exact contig at which failure occurs varies according to the parameters applied to dmrseq but also crops up. I have filtered out contigs less than 1000bp.

The experiment is a complex design with 48 replicates total and fails when testing 'Food' against 'Age' and 'Strain' as adjustCovariates:

testFoodCovariate<-"Food"
matchStrainAgeCovariate<-c("Strain","Age")
Food <- dmrseq(bs= bismarkBSseq.filtered, cutoff = 0.05, testCovariate=testFoodCovariate,adjustCovariate=matchStrainAgeCovariate,maxPerms = 10)

Food	Age	Strain
H	O	C32
H	O	C32
H	O	C32
H	O	C32
H	O	C32
H	O	C32
L	O	C32
L	O	C32
L	O	C32
L	O	C32
L	O	C32
L	O	C32
H	Y	C32
H	Y	C32
H	Y	C32
H	Y	C32
H	Y	C32
H	Y	C32
L	Y	C32
L	Y	C32
L	Y	C32
L	Y	C32
L	Y	C32
L	Y	C32
H	O	KA53
H	O	KA53
H	O	KA53
H	O	KA53
H	O	KA53
H	O	KA53
L	O	KA53
L	O	KA53
L	O	KA53
L	O	KA53
L	O	KA53
L	O	KA53
H	Y	KA53
H	Y	KA53
H	Y	KA53
H	Y	KA53
H	Y	KA53
H	Y	KA53
L	Y	KA53
L	Y	KA53
L	Y	KA53
L	Y	KA53
L	Y	KA53
L	Y	KA53

Bioconductor packages are up to date. Why do you think this error is occurring?

Thanks for any help!

[kdkorthauer]

Hi @jckhearn,

Would you mind sending me a small subset of your bsseq object (as an rds file) that throws the error so that I can see what's going on? Just a single chromosome or contig is sufficient, as long as it throws the error.

You can send to keegan@jimmy.harvard.edu if you'd prefer.

Thank you!
Best,
Keegan

[jckhearn]

Will do over the next couple of days!
Thanks,
Jack