filterGMM: Filter peptide microarray data

In katenambiar/pmpa: Peptide Microarray Pre-Processing and Analysis

Description

filterGMM is a function that filters peptide array data by identifying probes that specifically bind the secondary antibody and probes that are unreactive on the sample array. It does this by fitting a 2 component gaussian mixture model to the signal data from an array incubated with just secondary antibody (control array). Probes with signal exceeding the value of the cutoff quantile are flagged as secondary antibody binders.

Usage

filterGMM(arraydata, controldata, cutoff.quantile = 0.99, plot = TRUE,
  lhist = 50, num.dnorm = 5 * lhist, xlab = "", ylab = "",
  plottitle = "", xsize = 1, colramp = colorRampPalette(rev(brewer.pal(11,
  "RdYlBu"))), cleanup = TRUE, ...)

Arguments

arraydata	Vector of log transformed normalised signal intensities from the sample array
controldata	Vector of log transformed normalised signal intensities from the control array (incubated with just secondary antibody). Must be same the length as arraydata.
cutoff.quantile	Value indicating quantile of 1st gaussian distribution to set as a cutoff point. Defaults to 0.99

Value

logical vector of the same length as arraydata (TRUE = valid probes, FALSE = filtered probes)

katenambiar/pmpa documentation built on May 20, 2019, 7:41 a.m.