arraySecFilter-methods: Filter Secondary Antibody Binding Peptide Probes

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

Description

Implements filtering of signal from peptides that specifically bind to the secondary antibody. Using a control array incubated just with the secondary antibody, significantly binding probes are identified by fitting the data to a two-component Gaussian general mixture model. The signal intensity cutoff is set can be set at any point but defaults to the 95th percentile of the distribution from the non-binding peptides. Any probes showing signal greater than the cutoff are excluded.

Usage

arraySecFilter(x, ...)

## S4 method for signature 'MultiSet'
arraySecFilter(x, control.arrays, bg.offset = 1024,
  control.probes = NULL, cutoff.quantile = 0.95, remove.probes = TRUE,
  remove.control.arrays = TRUE)

Arguments

x	MultiSet object after background correction and log transformation
...	further arguments passed to hist
control.arrays	Numeric vector specifying negative control (secondary antibody only) arrays.
bg.offset	A positive constant to offset the foreground signal prior to subtractive background correction. Improves variance stabilisation for low intensity signal. See arrayBGcorr.
cutoff.quantile	Percentile of the non-binding distributiion to set a cutoff (default = 0.95)
removecontrol.arrays	either TRUE to remove the control array after filtering or FALSE to leave the control array in the dataset. (default = TRUE)
plot	Either TRUE to return a histogram with overlying density plots of the two mixture components on the current graphics device, or FALSE to implement the filtration without returning a plot. (default = FALES)

Value

MultiSet object filtered to remove probes with high secondary binding

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