lpm_MAplot: Plot an MA plot.

In goat-anti-rabbit/labelpepmatch.R: Tools For Interpreting Mass Spectra With Labeled Peptides

Description

Make MA plot of lpm_statlist object. An MA plot is a Bland-Altman plot where for every peak pair, the average (A) log2 quantity value of a feature is plotted in function of the difference (M) of log2 quantity. This is the ideal way of visualizing possible label bias over the entire continuum of quantities. Bias always needs some further investigation, but should, given a sufficient number of replicates, never be a big reason to worry. The bias can either be dealt with by accounting for label effect in a linear model (see lpm_linearmodel) or by normalizing the data within and between runs (see limma). The function also draws a loess fit.

Usage

lpm_MAplot(x, loess_span = 0.75, run = NULL)

Arguments

x	An object of class lpm_statlist
loess_span	Numeric. Span of the loess fit through the MA plot. See loess.
run	Integer. Choose the run that you want to visualize. If not specified, all runs are printed.

Author(s)

Rik Verdonck

goat-anti-rabbit/labelpepmatch.R documentation built on May 17, 2019, 7:29 a.m.