applies a function to 'databel' object...

apply2dfo {DatABEL} R Documentation

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", "glm", "coxph") and "process_simple_output" (process output from "sum", "prod", "sum_not_NA" [no. non-missing obs], "sum_NA" [no. missing obs.])
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*")

[Package DatABEL version 0.9-2 Index]