ProbeTrack: ProbeTrack

Description

This track can be used to display the frequency of antibody binding for each probe on an arrayas predicted by pepStat's function makeCalls.

Usage

ProbeTrack(sequence, intensity, probeStart, restab = NULL, group = NULL, name = "ProbeTrack", ...)

Arguments

sequence

A character vector. The sequence of peptides to display.

intensity

A numeric vector. The frequency of binding or the baseline corrected intensity for the peptides.

probeStart

A numeric vector. The start position of the peptides.

name

A character. The name of the track used in the title panel when plotting

restab

A data.frame containing all the above parameters, as outputted by pepStat's restab function.

group

A character. The group to display on the ProbeTrak. This is only required when restab is not NULL. See details section for more information.

...

Arguments to be passed to DataTrack.

Slots

sequence: A character vector. The probes sequence.
probeStart: A numeric vector. The start position of the probes.
intensity: A numeric vector. The frequency of response of each probe. Or the baseline corrected intensity of the signal.

Details

The vectors for the arguments sequence, freq and probeStart should be of the same length. If restab is provided, the three previous arguments will be ignored and group must be specified. group must be a valid column name in restab, data.frame.

Examples

Run this code

if(require(pepDat)){
  data(restab)
  pt <- ProbeTrack(sequence = restab$peptide,
                   intensity = restab$group2,
                   probeStart = restab$start)
  plotTracks(pt)
  plotTracks(pt, from = 460, to = 560, legend=TRUE)
}