aafTable-class: Class aafTable, a tabular microarray data class
Description
A class for storing and flexible output of microarray data to
HTML and text formats.
Objects from the Class
Objects are generally created by any of the annotation table constructors
that are also part of this package. Objects can also be created manually
by calls of the form new("aafList", probeids, table).Slots
probeids:-
Object of class
character containing the probe ids
for each row of the table.
table:-
Object of class
list containing aafList objects
all of the same length, representing the columns of the table.
Each item in the list must have a unique name.
Methods
- probeids
-
(aafTable): Returns a character vector containing the probe
ids for each row of the table.
- probeids<-
-
(aafTable): Sets the probe ids for the table rows. Can be
set to
character(0) if unknown or not applicable.
- colnames
-
(aafTable): Returns a character vector containing the names
of the columns stored in the table.
- colnames<-
-
(aafTable): Set the column names for the table. Each must be
unique.
- dim
-
(aafTable): Returns the dimensions of the table.
- merge
-
(aafTable, aafTable, all = FALSE, all.x = all, all.y = all,
suffixes = c(".x",".y")): Merges two
tables together, aligning common probe ids if possible.
Duplicate column names are given suffixes to make them unique.
Returns the merged table.
- rbind
-
(aafTable, aafTable, ...): Vertically combines tables by row.
Requires that column names be identical and that all tables
either have probe ids defined or not.
- [
-
Returns a subset of the table based on [row, column]. Indices
may be passed as integers or probe ids/column names.
- [[
-
Returns the given table column. This also supports recursive
subsetting to address columns, then cells, then sub-cells
(if applicable). See Extract for more information.
- \$
-
Returns the given table column.
- saveHTML
-
(aafTable, filename, title = "Bioconductor Affymetrix Probe
Listing", colnames = colnames(aafTable), range = 1:dim(aafTable)[1],
open = FALSE, widget = FALSE): Saves the table to HTML with
the specified filename and title. Both the columns and the
range of table rows can be specified. Range can either be
specified as a character vector of probe ids or an integer
vector of row positions. One can also specify whether to open
the resulting file in the browser and whether to use a widget
for column selection.
- saveText
-
(aafTable, filename, header = TRUE, colnames = colnames(aafTable),
range = 1:dim(aafTable)[1], widget = FALSE): Saves the table
to tab delimited text with specified filename and optional
header. Both the columns and the range of table rows can be
specified. Range can either be specified as a character
vector of probe ids or an integer vector of row positions.
One can also specify whether to use a widget for column
selection.