annotationListToMatrix {clValid}

Change annotation list to matrix

Description

Change biological functional annotation from list to TRUE / FALSE matrix

Usage

annotationListToMatrix(annotation, genenames)

Arguments

annotation

functional annotation of genes, as a list

genenames

vector of genenames

Details

Converts biological annotation from “list” to “matrix” format. In “list” format, each item in the list is a vector giving genes belonging to a particular biological class. In “matrix” format, each column is a logical vector indicating which genes belong to the biological class. Both BHI and BSI use the TRUE / FALSE matrix format for inputting predetermined biological functional classes.

Value

A logical matrix, where each element indicates whether the gene in row i belongs to the biological functional class of column j

Note

Special thanks to Rainer Machne, who initially suggested this change.

Author(s)

Guy Brock

See Also

BHI, BSI

Examples

data(mouse)
express <- mouse[1:25,c("M1","M2","M3","NC1","NC2","NC3")]
rownames(express) <- mouse$ID[1:25]
fc <- tapply(rownames(express),mouse$FC[1:25], c)
fc <- fc[-match( c("EST","Unknown"), names(fc))]
fc <- annotationListToMatrix(fc, rownames(express))

## see package vignette for example use when reading from Excel file