Error adjusting for cell counts in DNAmAge()

[cewim]

Hello,

I have encountered an error while attempting to use DNAmAge() to obtain DNAmAge, AgeAcDiff, IEAA, and EEAA from a methylation dataset.

I'm running the code below:

DNAmAge(Beta,
                         clocks=c("Horvath"),
                         toBetas=FALSE,
                         cell.count=TRUE,
                         cell.count.reference = "blood gse167998",
                         age=60,
                         min.perc=0.25)

The error I receive is:

Error in DNAmAge(Beta, clocks = c("Horvath"), toBetas = FALSE, cell.count = TRUE,  : 
  cell counts cannot be estimated since
                meffilEstimateCellCountsFromBetas function is giving an error.
                Probably your data do not have any of the required CpGs for that
                reference panel.
In addition: Warning message:
In knnimp(x, k, maxmiss = rowmax, maxp = maxp) :
  40589 rows with more than 50 % entries missing;
 mean imputation used for these rows

The error appears to indicate that I do not have the appropriate CpGs for "blood gse167998."

However, I know that my beta matrix contains the CpGs in Salas et al. 2022 because I used the FlowSorted.BloodExtended.EPIC dataset to perform leukocyte deconvolution on this dataset.

This also happens when I try to use other reference sets, e.g., Salas' "blood idoloptimized epic."

I took a look at the meffilEstimateCellCountsFromBetas function within DNAmAge() using trace("DNAmAge", edit=T). I thought maybe this error was thrown because meffilEstimateCellCountsFromBetas() is now meffil.estimate.cell.counts.from.betas().

I updated the name of the meffil function in DNAmAge(). Unfortunately, the same error occurred.

Will you please assist me in figuring out why this is happening?

Also, am I able to provide my own cell type estimates?

Thank you very much!

Courtney