limma (version 3.22.7)

readSpotTypes: Read Spot Types File

Description

Read a table giving regular expressions to identify different types of spots in the gene-dataframe.

Usage

readSpotTypes(file="SpotTypes.txt",path=NULL,sep="\t",check.names=FALSE,...)

Arguments

file

character string giving the name of the file specifying the spot types.

path

character string giving the directory containing the file. Can be omitted if the file is in the current working irectory.

sep

the field separator character

check.names

logical, if FALSE column names will not be converted to valid variable names, for example spaces in column names will not be left as is

...

any other arguments are passed to read.table

Value

A data frame with columns

SpotType

character vector giving names of the spot types

ID

character vector giving regular expressions

Name

character vector giving regular expressions

Color

character vector giving names of colors

Details

The file is a text file with rows corresponding to types of spots and the following columns: SpotType gives the name for the spot type, ID is a regular expression matching the ID column, Name is a regular expression matching the Name column, and Color is the R name for the color to be associated with this type.

See Also

An overview of LIMMA functions for reading data is given in 03.ReadingData.