ProbeTrack: ProbeTrack
In Pviz: Peptide Annotation and Data Visualization using Gviz

Description Usage Arguments Details Slots Author(s) See Also Examples

View source: R/AllClasses.R

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

1 2	ProbeTrack(sequence, intensity, probeStart, restab = NULL, group = NULL, name = "ProbeTrack", ...)

`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`.

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.

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.

Renan Sauteraud

GdObject

restab

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)
}