Layout: The Layout class

Description Usage Arguments Details Fields and Methods Note Author(s) See Also Examples

Description

Package: aroma
Class Layout

Object
~~|
~~+--Layout

Directly known subclasses:
GalLayout

public static class Layout
extends Object

The Layout class describes the layout of a microarray slide, such as the number of spots and the layout of the grids etc. A microarray slide is layout in a number of grids, where each grid is refered to by its row and its column. Within each grid, each spot is refered to by its row and its column within that grid. For example, a microarray slide with 4*3 grids and where each grid has 12*10 spots, has in total 4*3*12*10 = 12*120 = 1440 spots. The spot in the top left corner is located at grid (1,1) and spot (1,1) and we say it has the location (1,1,1,1). In the above example, the spot in the lower right corner of the slide has the location (4,3,12,10). Further more, each spot on a microarray slide has a unique index. This index starts counting starts with grid 1, moves along row 1 from column 1 until the last column, then advances to the next row. After all rows in grid 1 are indexed, counting proceeds to grid 2 and so on. This way of indexing the spots is used by for instance GenePix, Spot and ScanAlyze. Continuing the example above, the spot at location (1,1,1,1) has index 1, the spot at location (4,3,12,10) has index 1440. The spot at location (2,2,11,3) has index ((2-1)*3+(2-1))*12*10+(11-1)*10+3 = 483. To get the index from a location one do getIndex(layout, 2,2,11,3) where layout <- Layout(4,3,12,10). To get the location from a index one do getLocation(layout, 483), which gives the vector (2, 2, 11, 3). To get the position, i.e. the overall row and column of a spot on the microarray slide one can do getPosition(483) which give the position (23,13).

All spots are refered to by their unique indices.

Usage

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Layout(ngrid.r=0, ngrid.c=0, nspot.r=0, nspot.c=0, geneSpotMap=NULL, name=NULL, id=NULL, plate=NULL, printorder=NULL)

Arguments

nspot.r

The number of rows of spots per grid. This first argument can also be a list containing the fields nspot.r, nspot.c, ngrid.r, and ngrid.c.

nspot.c

The number of columns of spots per grid.

ngrid.r

The number of rows of grids per slide.

ngrid.c

The number of columns of grids per slide.

name

A vector of names for the spot. optional.

id

A vector of ids for the spot. optional.

printorder

A matrix or a character string specifying the order that spots where printed. For more details *setPrintorder().

geneSpotMap

.

plate

.

Details

GenBank Accession numbers, SwissProt/TrEMBL Accession numbers or Entry Names.

Fields and Methods

Fields

ngrid.r The number of rows of grids per slide.
ngrid.c The number of columns of grids per slide.
nspot.r The number of rows of spots in each grid.
nspot.c The number of columns of spots in each grid.
name A vector of strings which specified the name of each gene.
id A vector of strings which specified the id of each gene.

Methods:

anonymize -
as.character -
as.data.frame -
as -
as.Layout -
equals Checks if a Layout object is equals to some other object.
fromDataFrame -
getBlank -
getGeneGroups -
getId Gets the id of one or more spots.
getIndex Gets the index of a spot given its location.
getIndices Gets the indices of the spots at the given locations.
getLayoutGroupsByName -
getLocation Gets the location of a spot given its index.
getName Gets the name of one or more spots.
getPlate -
getPlateGroups -
getPlateNumber -
getPosition Gets the position of a set of spots given their indices.
getPrintdipGroups -
getPrintorder Gets the order of the spots in which they were printed.
getPrinttipGroups -
getSlideColumnGroups -
getSlideRowGroups -
gridSize Gets the number of spots in each grid.
hasIds -
hasNames -
hasPlates -
indexOf Gets the index of one or more spots from their name or id.
nbrOfColumns Gets the number of columns on a microarray.
nbrOfGrids Gets the number of grids on a microarray.
nbrOfPlates -
nbrOfReplicates -
nbrOfRows Gets the number of rows on a microarray.
nbrOfSpots Gets the size of a microarray.
put -
read Reads layout information from a tab-delimited file.
rename -
set Sets the layout.
setGeneGroups -
setId Sets the id of one or more spots.
setName Sets the name of one or more spots.
setPlate -
setPlateGroups -
setPrintdipGroups -
setPrintorder -
setPrinttipGroups -
setSlideColumnGroups -
setSlideRowGroups -
size Gets the size of a microarray.
toXYMatrix Layouts out values in the same way as the spots are layout.
write Writes the layout information to a tab-delimited file.

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstanciationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save

Note

There are several functions that returns a Layout object. It is only in very special cases that you have to create one yourself.

In the sma package some functions are related to this class. This, class might be backward compatible with these functions, but the reverse is not true. The following functions are known be related to this class: init.grid, id2image (and image2id).

Author(s)

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

See Also

MicroarrayData.getLayout.

Examples

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  layout <- Layout(ngrid.r=4, ngrid.c=4, nspot.r=18, nspot.c=18)

  SMA$loadData("mouse.setup")
  layout <- Layout(mouse.setup)
  # or, equivalent...
  layout <- as.Layout(mouse.setup)

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