runCaSpER error

[SaritaPoonia]

Getting below error in runCaSpER function: object <- CreateCasperObject(raw.data=data_raw,loh.name.mapping=loh.name.mapping, sequencing.type="single-cell", cnv.scale=3, loh.scale=3, matrix.type="normalized", expr.cutoff=0.1, annotation=rannotation, method="iterative", loh=loh, filter="median",
control.sample.ids=colnames(NKData1), cytoband=cytoband)

final.objects <- runCaSpER(object, removeCentromere=T, cytoband=cytoband, method="iterative") Performing recursive median filtering... Performing HMM segmentation... Error in manualSegment(correctOut$copy, chr, autosomes, param, maxiter, : INTEGER() can only be applied to a 'integer', not a 'NULL' Called from: manualSegment(correctOut$copy, chr, autosomes, param, maxiter, verbose) Error during wrapup: unimplemented type (29) in 'eval'

Error: no more error handlers available (recursive errors?); invoking 'abort' restart Error during wrapup: INTEGER() can only be applied to a 'integer', not a 'unknown type #29' Error: no more error handlers available (recursive errors?); invoking 'abort' `restart```

[kenminsoo]

For anyone with this error,

Make sure that the loh.name.mapping dataframe has the following properties loh.name is the names of samples as they are from the BAF file—i.e. ie sample.baf, sample.snp —this might be the case if you used a different suffix

sample.name is the names of samples as they are in the count dataframe—the column names.

Otherwise your R will crash.