merge_spectra_opts: Merge default spectra processing options
In krisrs1128/phyloseqExtend: Extend Phyloseq to Rich Data Types

Merge default spectra processing options

1	merge_spectra_opts(opts = list())

opts

A partially filled list specifying options to spectra processing. Those that are not specified will be merged according to their defaults below. These are, $align_opts Arguments passed to alignSpectra() in the MALDIquant package. Defaults to the default options for that function.
$baseline_opts Arguments passed to the removeBaseline() function in the MALDIquant package. Defaults to the default options for that function.
$binary Return a sample x potential-peak indicator matrix? Or just the peaks intensities [with zeros, if it was not a peak]? Defaults to FALSE.
$peak_opts Arguments passed to detectPeak() in the MALDIquant package. Defaults to the default options for that function.
$thresh_max The maximum value for any sample, above which we discard it as an outlier. Defaults to Inf (don't discard anything)

opts The version of opts with unspecified options filled in.

krisrs1128/phyloseqExtend documentation built on May 20, 2019, 1:31 p.m.