limma: readSpotTypes – R documentation

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limma

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`

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