DatABEL (version 0.9-2)

apply2dfo: applies a function to 'databel' object...

Description

applies a function to 'databel' object

Usage

apply2dfo(..., dfodata, anFUN="lm", MAR=2, procFUN, outclass="matrix",
    outfile, type="DOUBLE", transpose=TRUE)

Arguments

dfodata

'databel' object which is iterated over

anFUN

user-defined analysis function

MAR

which margin to iteracte over (default = 2, usually these are 'columns' used to store SNP data)

procFUN

function to process the output and present that as a fixed-number-of-columns matrix or fixed-length vector. Can be missing if standard functions listed below are used. Pre-defined processors included are "process_lm_output" (can process functions "lm",

outclass

output to ("matrix" or "databel")

outfile

if output class is "databel", the generated object is bond to the outfile

type

if output class is "databel", what data tyoe to use for storage

transpose

whether to transpose the output

...

arguments passed to the anFUN

Details

An iterator applying a user-defined function to an object of 'databel-class' object

Examples

unlink("tmp*")
a <- matrix(rnorm(50),10,5)
rownames(a) <- paste("id",1:10,sep="")
colnames(a) <- paste("snp",1:5,sep="")
b <- as(a,"databel")
apply(a,FUN="sum",MAR=2)
apply2dfo(SNP,dfodata=b,anFUN="sum")
tA <- apply2dfo(SNP,dfodata=b,anFUN="sum",outclass="databel",outfile="tmpA")
tA
as(tA,"matrix")
apply2dfo(SNP,dfodata=b,anFUN="sum",transpose=FALSE)
tB <- apply2dfo(SNP,dfodata=b,anFUN="sum",transpose=FALSE,outclass="databel",outfile="tmpB")
tB
as(tB,"matrix")

sex <- 1*(runif(10)>.5)
trait <- rnorm(10)+sex+as(b[,2],"vector")+as(b[,2],"vector")*sex*5
apply2dfo(trait~SNP*sex,dfodata=b,anFUN="lm")
tC <- apply2dfo(trait~SNP*sex,dfodata=b,anFUN="lm",outclass="databel",outfile="tmpC")
tC
as(tC,"matrix")
apply2dfo(trait~SNP*sex,dfodata=b,anFUN="lm",transpose=FALSE)
tD <- apply2dfo(trait~SNP*sex,dfodata=b,anFUN="lm",transpose=FALSE,outclass="databel",outfile="tmpD")
tD
as(tD,"matrix")
rm(tA,tB,tC,tD)
gc()
unlink("tmp*")