getIndices.Layout: Gets the indices of the spots at the given locations

In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description

Gets the indices of the spots at the given locations. This method is very useful for instance when one would like to look for spatial effects such as edge effects etc.

Usage

## S3 method for class 'Layout'
getIndices(this, gridRows=NULL, gridColumns=NULL, spotRows=NULL, spotColumns=NULL, ...)

Arguments

gridRows	The grid rows to be included. If NULL all are included.
gridColumns	The grid column to be included. If NULL all are included.
spotRows	The spot rows to be included. If NULL all are included.
spotColumns	The spot column to be included. If NULL all are included.

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

Examples

  SMA$loadData(c("mouse.data", "mouse.setup"))
  raw <- RawData(mouse.data, layout=as.Layout(mouse.setup))
  ma <- getSignal(raw)
  layout <- getLayout(ma)

  plotSpatial(ma)

  # Highlights all spots in grid (1,2)
  idx <- getIndices(layout, gridRows=1, gridColumns=2);
  highlight(ma, idx, col="purple")

  # Highlight all spots in column 1, 6 and 12 in
  # grid (3,2), (3,3), (4,2) and (4,3).
  idx <- getIndices(layout, gridRows=3:4, gridColumns=2:3, spotColumns=c(1,6,12));
  highlight(ma, idx, col="orange")

  # Highlight all "alley spots" of each printtip group, i.e. those spots that
  # do *not* have eight neighbors and do a background "alley" next to them.
  alley <- getIndices(layout, spotRows=c(1,layout$nspot.r))
  alley <- union(alley, getIndices(layout, spotColumns=c(1,layout$nspot.c)));
  highlight(ma, alley, col="pink")

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.