readSpotTypes: Read Spot Types File

In limma: Linear Models for Microarray Data

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

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.

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

Author(s)

Gordon Smyth following idea of James Wettenhall

See Also

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

limma documentation built on Nov. 8, 2020, 8:28 p.m.