Error in validObject(.Object) : invalid class "ScoreMatrix" object: superclass "mMatrix" not defined in the environment of the object's class

[danli349]

Hello

How should I solve this problem?

library(genomation)
transcriptFile=system.file("extdata",
                      "refseq.hg19.chr20.bed",
                      package="compGenomRData")
feat=readTranscriptFeatures(transcriptFile,
                            remove.unusual = TRUE,
                            up.flank = 500, down.flank = 500)
prom=feat$promoters # get promoters from the features


# get for H3K4me3 values around TSSes
# we use strand.aware=TRUE so - strands will
# be reversed
H3K4me3File=system.file("extdata",
                      "H1.ESC.H3K4me3.chr20.bw",
                      package="compGenomRData")
sm=ScoreMatrix(H3K4me3File, prom,
               type="bigWig", strand.aware = TRUE)

Error in validObject(.Object) : 
  invalid class "ScoreMatrix" object: superclass "mMatrix" not defined in the environment of the object's class

Thanks a lot

[igumnov-daniel]

Possible solution: https://github.com/BIMSBbioinfo/genomation/issues/209

[danli349]

@igumnov-daniel It works! Thanks