I am having a bit of trouble getting an MAplot from a result subset (though ?plotMA says this is possible) of a DESeq2 dataset. I am doing the following and getting this error:

> plotMA(BN_group_female_padj.01, alpha = .01, contrast=c("group", "femaleBB", "femalevehicle") ,ylim=c(-10,10))
Error in plotMA(BN_group_female_padj.01, alpha = 0.01, contrast = c("group",  : 
  Error from the generic function 'plotMA' defined in package 'BiocGenerics': no S4 method definition for argument 'BNST_group_female_padj.01' of class 'GRanges' was found. Did you perhaps mean calling the function 'plotMA' from another package, e.g. 'limma'? In that case, please use the syntax 'limma::plotMA'.

I can plot it from the entirety of the DEseqDataSet however I can't seem to find a way to only plot sites below a specific padj?

Thanks!

plotMA is designed for data.frame-like objects, but here you have a GRanges.

You can get the relevant three columns from the GRanges object using `$`:

df <- data.frame(gr$baseMean, gr$log2FoldChange, gr$padj < 0.1)

Check help("plotMA","geneplotter"):

  object: A ‘data.frame’ with (at least) three columns, the first
          containing the mean expression values (for the x-axis), the
          second the logarithmic fold change (for the-y axis) and the
          third a logical vector indicating significance (for the
          colouring of the dots).