You are loosing a lot of time by repeatedly calculating character
indices with paste() in every iteration. Two options:
-- 1) calculate these once outside the loop and then refer to them by
index
idx.names <- vector(mode="character", length=nind)
for (i in (0:(nind-1))) {idx[i+1] <- # need the offset
c(paste("G_hat_0_",i,sep=""),
paste("G_hat_1_",i,sep=""),
paste("G_hat_2_",i,sep=""),
paste("G_",i,sep="") ) }
Then the inner loop would be:
for (i in (0:(nind-1))) {
Gmax = which.max(c(data[[ idx.names[1] ]][row],
data[[ idx.names[2] ]][row],
data[[ idx.names[3] ]][row] ))
Gtru = data[[ idx.names[4] ]][row] + 1 # add 1 to match Gmax range
}
And as has been said many times before,...
require(fortunes)
fortune("dog")
-- 2) probably even faster to pre-calculate (or just construct by
inspection) those column indices as a numeric vector and use then
access with data[row, numidxs[i] ]
The for-loop is generally going to be faster than an lapply solution.
The fastest solution would be a fully indexed strategy, which might
become more apparent (it's not yet so to me) after you implement the
second option above.
--
David.
On Oct 8, 2010, at 11:35 AM, epowell wrote:
My data looks like this:
data
name G_hat_0_0 G_hat_1_0 G_hat_2_0 G_0 G_hat_0_1 G_hat_1_1
G_hat_2_1 G_1
1 rs0 0.488000 0.448625 0.063375 1 0.480875 0.454500
0.064625 1
2 rs1 0.002375 0.955375 0.042250 1 0.000000 0.062875
0.937125 2
3 rs2 0.050375 0.835875 0.113750 1 0.877250 0.115875
0.006875 0
4 rs3 0.000000 0.074750 0.925250 2 0.897750 0.102000
0.000250 0
5 rs4 0.000125 0.052375 0.947500 2 0.261500 0.724125
0.014375 1
6 rs5 0.003750 0.092125 0.904125 2 0.023000 0.738125
0.238875 1
And my task is:
For each individual (X) on each row, to find the index corresponding
to the
max of G_hat_X_0, G_hat_X_1, G_hat_X_2 and then increment the cell
of the
confusion matrix with the row corresponding to that index and the
column
corresponding to G_X.
For example, in the first row and the first individual, the index
with the
max value (0.488000) is 0 and the G_0 value is 1, so I would increment
matrix index of the first row and second column. (Note that the ranges
between rows and columns are one off. That is accounted for in the
code.)
In reality the data will be much bigger, containing 10000 rows and a
variable number of columns (inds) between 10 and 500.
The correct result is:
cmat
tru_rr tru_rv tru_vv
call_rr 2 2 0
call_rv 0 4 0
call_vv 0 0 4
I am not sure what the best way to do this is. I implemented it
once using
two for loops. Then I tried to use lapply and came up with a nested
lapply
solution, but it was slower than the simple loops. I still think
that there
is a better way and I was hoping for some advice. Perhaps something
with
pmax....
#### DATA PREP ##########
data = data.frame(name=c("rs0","rs1","rs2","rs3","rs4","rs5"),
G_hat_0_0=c(0.488,0.002375,0.050375,0,0.000125,0.00375),
G_hat_1_0=c(0.448625,0.955375,0.835875,0.07475,0.052375,0.092125),
G_hat_2_0=c(0.063375,0.04225,0.11375,0.92525,0.9475,0.904125),
G_0=c(1,1,1,2,2,2),
G_hat_0_1=c(0.480875,0,0.87725,0.89775,0.2615,0.023),
G_hat_1_1=c(0.4545,0.062875,0.115875,0.102,0.724125,0.738125),
G_hat_2_1=c(0.064625,0.937125,0.006875,0.00025,0.014375,0.238875),
G_1=c(1,2,0,0,1,1))
# get list of inds in file (e.g. G_0,G_1,...,G_100)
inds = grep("G_[0-9]+",names(data),perl=T,value=T)
# get total number of inds
nind = length(inds)
# create an empty "confusion" table
cmat = matrix(rep(0,9), nrow=3, ncol=3)
colnames(cmat) = c("tru_rr", "tru_rv", "tru_vv")
rownames(cmat) = c("call_rr","call_rv","call_vv")
## APPROACH 1: Nested For Loop ####
# Nested Loop Approach
for (row in (1:nrow(data))) {
for (i in (0:(nind-1))) {
Gmax = which.max(c( data[[paste("G_hat_0_",i,sep="")]][row],
data[[paste("G_hat_1_",i,sep="")]][row],
data[[paste("G_hat_2_",i,sep="")]][row] ))
Gtru = data[[paste("G_",i,sep="")]][row] + 1 # add 1 to match Gmax
range
cmat[Gmax,Gtru] = cmat[Gmax,Gtru] + 1
}
}
## APPROACH 2: Nested lapply ####
# This routine finds the geno w/ highest prob from the erg.avgs.
# and compares it to the true geno. Result is tallied by
# incrementing the appropriate index of the confusion matrix
add2cmat <- function(ind,locus) {
Gmax = which.max(c( data[[paste("G_hat_0_",ind,sep="")]][locus],
data[[paste("G_hat_1_",ind,sep="")]][locus],
data[[paste("G_hat_2_",ind,sep="")]][locus] ))
Gtru = data[[paste("G_",ind,sep="")]][locus] + 1 # add 1 to match
Gmax
range
cmat[Gmax,Gtru] <<- cmat[Gmax,Gtru] + 1 # use double arrow to
modify
global env.
}
# Run add2cmat for all individuals on a given locus
add_locus2cmat <- function(locus) {
lapply(0:(nind-1),add2cmat,locus)
}
junk = lapply((1:nrow(data)),add_locus2cmat) # don't need return
value
--
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David Winsemius, MD
West Hartford, CT
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