Class aafTable, a tabular microarray data class

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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.

Author(s)

Colin A. Smith, annaffy@colinsmith.org

See Also

aafTable, aafTableFrame, aafTableAnn, aafTableInt

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