process_spectra: Wrapper for processing spectra matrices

In krisrs1128/phyloseqExtend: Extend Phyloseq to Rich Data Types

Description

This function 1) removes outliers, 2) removes spectra baseline, 3) aligns spectra, and 3) detects peaks, across samples in a spectrum.

Usage

process_spectra(X, opts = list())

Arguments

X	A spectra matrix with samples on rows.
opts	A potentially partially specified list of processing options. See merge_spectra_opts() for options and defaults.

Value

A list with the followign objects $X The spectra matrix with peaks aligned.
$peaks_ix A list whose i^th element give the indices of peaks in the i^th sample.
$X_peaks A matrix whose columns are the positions where a peak was detected in at least one sample.
$X_peaks_zeros The same as X_peaks, but with zeros for samples where that given position was not identified as a peak.

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