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

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.

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.

Author(s)

Renan Sauteraud

See Also

GdObject

restab

Examples

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)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Pviz)
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Pviz/ProbeTrack.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ProbeTrack
> ### Title: ProbeTrack
> ### Aliases: ProbeTrack ProbeTrack-class
> 
> ### ** Examples
> 
> 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)
+ }
Loading required package: pepDat
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>