A convenience function that builds an ExprsArray
object.
arrayExprs(object, colBy, include, colID, begin, ...)
What to import as an ExprsArray
object. See Details.
A numeric or character index. The column that contains group annotations.
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.
A numeric or character index. The column used to name subjects.
For data.frame
or file import only.
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.
An ExprsArray
object.
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
.