exprso (version 0.1.7)

arrayExprs: Import Data as ExprsArray

Description

A convenience function that builds an ExprsArray object.

Usage

arrayExprs(object, colBy, include, colID, begin, ...)

Arguments

object

What to import as an ExprsArray object. See Details.

colBy

A numeric or character index. The column that contains group annotations.

include

A list of character vectors. Specifies which annotations in colBy to include in which groups. Each element of the list specifies a unique group while each element of the character vector specifies which annotations define that group. For binary classification, the first list element defines the negative, or control, group.

colID

A numeric or character index. The column used to name subjects. For data.frame or file import only.

begin

A numeric scalar. The j-th column at which feature data starts. For data.frame or file import only.

...

Additional arguments passed along to read.delim. For file import only.

Value

An ExprsArray object.

Details

Importing a data.frame object:

This function expects that the imported data.frame has the following format: rows indicate subject entries while columns indicate measured variables. The first several columns should contain annotation information (e.g., age, sex, diagnosis). The remaining columns should contain feature data (e.g., expression values). The argument begin defines the j-th column at which the feature data starts. This function automatically removes any features with NA values. Take care to remove any factor columns before importing.

Importing an ExpressionSet object:

The package Biobase maintains a popular class object called ExpressionSet that often gets used to store expression data. This function converts this eSet object into an ExprsArray object. This function automatically removes any features with NA values.

Importing a file:

arrayExprs can also build an ExprsArray object from a tab-delimited data file, passing along the file and ... argument(s) to read.delim. All rules for data.frame import also apply here. By default, arrayExprs forces stringsAsFactors = FASE.

See Also

ExprsArray-class, GSE2eSet