GetTongs: Generate and visualize the tongs plot

In AffyRNADegradation: Analyze and correct probe positional bias in microarray data due to RNA degradation

Description

The tongs plot and the related degradation hook show the relationship between expression level and probe location bias. They are required for the correct estimation of RNA degradation effects.

Usage

GetTongs(affyData, chip.idx = 1)
PlotTongs(tongs)
PlotDegradationHooks(affyData, ...)

Arguments

affyData	an AffyBatch object.
chip.idx	index of the sample to compute the tongs for.
tongs	the tongs plot data table.
...	optional graphical parameters.

Value

Tongs

a table containing Tongs plot values ordered by expression level.

Author(s)

Mario Fasold

Examples

if (require(AmpAffyExample)) {
  # Get example data
  data(AmpData)

  tongs <- GetTongs(AmpData, chip.idx = 4)
  PlotTongs(tongs)

  PlotDegradationHooks(AmpData[,c(3,4)])
}

Example output

Loading required package: affy
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Loading required package: AmpAffyExample
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'AmpAffyExample'

AffyRNADegradation documentation built on Nov. 8, 2020, 5:36 p.m.