DatABEL (version 0.0-7)

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

Description

applies a function to 'databel_filtered_R' object

Usage

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

Arguments

dfodata

'databel_filtered-R' 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_filtered_R")

outfile

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

type

if output class is "databel_filtered_R", 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 databel_filtered_R - class object

Examples

a <- matrix(rnorm(50),10,5)
rownames(a) <- paste("id",1:10,sep="")
colnames(a) <- paste("snp",1:5,sep="")
b <- as(a,"databel_filtered_R")
apply(a,FUN="sum",MAR=2)
apply2dfo(SNP,dfodata=b,anFUN="sum")
tA <- apply2dfo(SNP,dfodata=b,anFUN="sum",outclass="databel_filtered_R",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_filtered_R",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_filtered_R",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_filtered_R",outfile="tmpD")
tD
as(tD,"matrix")