getLayout {limma}R Documentation

Extract the Print Layout of an Array from the GAL File

Description

From the Block, Row and Column information in the GAL file, determine the number of grid rows and columns on the array and the number of spot rows and columns within each grid.

Usage

getLayout(gal, guessdups=FALSE)

Arguments

gal data.frame containing the GAL, i.e., giving the position and gene identifier of each spot
guessdups logical, if TRUE then try to determine number and spacing of duplicate spots, i.e., within-array replicates

Details

A Gene Allocation List (GAL) file is a list of genes and associated information produced by an Axon microarray scanner. This function assumes that the data.frame contains columns Block, Column and Row. The number of tip columns is not determinable from the GAL but is assumed to be four.

Value

A list with components

ngrid.r integer, number of grid rows on the arrays
ngrid.c integer, number of grid columns on the arrays
nspot.r integer, number of rows of spots in each grid
nspot.c integer, number of columns of spots in each grid

Author(s)

Gordon Smyth

See Also

gpTools.

An overview of LIMMA functions for reading data is given in 3.ReadingData.

Examples

# gal <- readGAL()
# layout <- getLayout(gal)

[Package limma version 1.6.7 Index]