Error in 4.3 Sex prediction section

[pedrodcb]

This code:

predictedSex <- getSex(GRset, cutoff = -2)$predictedSex
predictedSex

plotSex(getSex(GRset, cutoff = -2))

Should be this:

predictedSex <- getSex(GRset, cutoff = -2)
predictedSex

GRset <- addSex(GRset, sex = predictedSex)

plotSex(GRset)

If not the following error is returned when running plotSex(getSex(GRset, cutoff = -2)):
Error in h(simpleError(msg, call)) : error in evaluating the argument 'table' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'colnames': unable to find an inherited method for function ‘colData’ for signature ‘"DFrame"’

Cheers!

[MEFarhadieh]

Try the code below:

sex_prediction <- getSex(GRset, cutoff = -2)

if (!all(c("predictedSex", "xMed", "yMed") %in% colnames(colData(GRset)))) {
  colData(GRset)$predictedSex <- sex_prediction$predictedSex
  colData(GRset)$xMed <- sex_prediction$xMed
  colData(GRset)$yMed <- sex_prediction$yMed
}

col_data <- as.data.frame(colData(GRset))

plotSex(GRset)