Monocle3/cicero - data loading in R

Question

[sidrah.maryam]

I am trying to run cicero on scATAC data, and while loading the data I am getting this error:

Error: CellDataSet 'phenoData' is class 'data.frame' but should be or extend 'AnnotatedDataFrame'

where the command was:

input_cds <- suppressWarnings(newCellDataSet(indata, + featureData = peakinfo, + phenoData = cellinfo, lowerDetectionLimit = 0.1, expressionFamily = VGAM::negbinomial.size()))

cellinfo- barcodes.tsv, peakinfo - peak.bed, indata - matrix.mtx

Please suggest what could be done.

[antonioggsousa]

Hi,

Did you run?

pd <- methods::new("AnnotatedDataFrame", data = cellinfo)

And then give this pd variable to the phenoData option. The new function will coerce the cellinfo data.frame to AnnotatedDataFrame class.

António