aroma.affymetrix (version 3.2.2)

SnpPlm: The SnpPlm interface class

Description

Package: aroma.affymetrix
Class SnpPlm

Interface
~~|
~~+--SnpPlm

Directly known subclasses:
AffineCnPlm, AffineSnpPlm, AvgCnPlm, AvgSnpPlm, CnPlm, HetLogAddCnPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiSnpPlm, RmaCnPlm, RmaSnpPlm

public class SnpPlm
extends Interface

An Interface implementing methods special for ProbeLevelModels specific to SNP arrays.

Usage

SnpPlm(...)

Arguments

...

Not used.

Methods

Methods:

	getCellIndices	-
	getChipEffectSet	-
	getMergeStrands	-
	getProbeAffinityFile	-
	setMergeStrands	-

Methods inherited from Interface:
extend, print, uses

Requirements

Classes inheriting from this Interface must provide the following fields:

mergeStrands

A logical value indicating if strands should be merged or not.

Author

Henrik Bengtsson

Examples

for (zzz in 0) {

# Setup verbose output
verbose <- Arguments$getVerbose(-2)
timestampOn(verbose)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Define an example dataset using this path
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Find any SNP dataset
path <- NULL
if (is.null(path))
  break

if (!exists("ds")) {
  ds <- AffymetrixCelSet$fromFiles(path)
}
print(ds)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Create a set of various PLMs for this dataset
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (!exists("models", mode="list")) {
  mergeStrands <- TRUE
  models <- list(
    rma = RmaSnpPlm(ds, mergeStrands=mergeStrands),
    mbei = MbeiSnpPlm(ds, mergeStrands=mergeStrands)
#   affine = AffineSnpPlm(ds, background=FALSE, mergeStrands=mergeStrands)
  )
}
print(models)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# For each model, fit a few units
#
# Note, by fitting the same set of units across models, the internal
# caching mechanisms of aroma.affymetrix makes sure that the data is
# only read into memory once. See log for reading speed.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
units <- 55+1:100

for (model in models) {
  ruler(verbose)
  fit(model, units=units, force=TRUE, verbose=verbose)
}

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# For each unit, plot the estimated (thetaB,thetaA) for all models
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Should we plot the on the log scale?
log <- TRUE

# Do only user to press ENTER if more than one unit is plotted
opar <- par(ask=(length(units) > 1))

Alab <- expression(theta[A])
Blab <- expression(theta[B])
if (log) {
  lim <- c(6, 16)
} else {
  lim <- c(0, 2^15)
}

# For each unit...
for (unit in units) {
  # For all models...
  for (kk in seq_along(models)) {
    ces <- getChipEffects(models[[kk]])
    ceUnit <- ces[unit]
    snpName <- names(ceUnit)[1]
    theta <- ceUnit[[1]]
    thetaA <- theta[[1]]$theta
    thetaB <- theta[[2]]$theta
    if (log) {
      thetaA <- log(thetaA, base=2)
      thetaB <- log(thetaB, base=2)
    }

    # Create the plot?
    if (kk == 1) {
      plot(NA, xlim=lim, ylim=lim, xlab=Blab, ylab=Alab, main=snpName)
      abline(a=0, b=1, lty=2)
    }

    # Plot the estimated parameters
    points(thetaB, thetaA, col=kk, pch=19)
  }
} # for (unit ...)

# Reset graphical parameter settings
par(opar)

} # for (zzz in 0)
rm(zzz)