I just wanted to put this out there. It's just some of my observations
about things that happen with R, or happened in this particular
investigation. There were definitely some lessons for me in this, and
maybe that will be true of someone else. The main thing I picked up is
that it is good to put plenty of checks into our code -- if we expect
input of a certain type or class, then I should either coerce input into
that structure or test the input and throw an error. If the function
works very differently for different kinds of input, this should be
documented. The more people are doing this, the better things will go
for everyone.
I was working with a CRAN package called RFGLS...
http://cran.r-project.org/web/packages/RFGLS/index.html
...and I was getting an error. After a few rounds of testing I realized
that the error was caused by a FAMID variable that was of character type.
The problem seemed to be that gls.batch() expected FAMID to be integers,
but the default ought to be character type because family and individual
IDs in nearly all genetic-analysis software are character strings (they
might even be people's names).
This was the error:
Error in sum(blocksize) : invalid 'type' (character) of argument
Calls: gls.batch -> bdsmatrix
To figure out more about it, I spent a bunch of time to go from CMD
BATCH mode to an interactive session so that I could look at
traceback(). That got me this additional info:
traceback()
2: bdsmatrix(sizelist, lme.out$sigma@blocks, dimnames = list(id, id))
bdsmatrix() is from a package on which RFGLS depends:
http://cran.r-project.org/web/packages/bdsmatrix/index.html
The problem is that RFGLS's gls.batch() function is sending something to
bdsmatrix's bdsmatrix() that it can't handle. So I look at the code for
bdsmatrix() and I see this:
if (any(blocksize <= 0))
stop("Block sizes must be >0")
if (any(as.integer(blocksize) != blocksize))
stop("Block sizes must be integers")
n1 <- as.integer(sum(blocksize))
The condition any(as.integer(blocksize) != blocksize)) fails (is TRUE)
only if blocksize contains one or more noninteger numeric values. It
doesn't fail if blocksize is character or logical if the character
strings are integers. Example:
4=="4"
[1] TRUE
That's an interesting feature of R, but I guess that's how it works.
Also this:
1=="1"
[1] TRUE
1==TRUE
[1] TRUE
"1"==TRUE
[1] FALSE
bdsmatrix() has no test that blocksize is numeric, so it fails when
sum(blocksize) cannot sum character strings.
Next I had to figure out where RFGLS's gls.batch() is going wrong in
producing sizelist. It is created in a number of steps, but I
identified this line as especially suspicious:
test.dat$famsize[test.dat$FTYPE!=6]=ave(test.dat$FAMID[test.dat$FTYPE!=6],test.dat$FAMID[test.dat$FTYPE!=6],FUN=length)
famsize was later converted to sizelist, and this line also includes
FAMID, so this is likely where the problem originates. Of course this
is the big problem with debugging -- it's hard to find the source of an
error that occurs far downstream in another function from a different
package. I see that ave() is used, so I have to understand ave().
William Dunlap provided some guidance:
"ave() uses its first argument, 'x', to set the length of its output and
to make an initial guess at the type of its output. The return value of
FUN can alter the type, but only in an 'upward' direction where
logical<integer<numeric<complex<character<list. (This is the same rule
that x[i]<-newvalue uses.)"
In other words, if x is of character type, the output cannot be of
integer or numeric type even if the output of FUN is always of integer
or numeric type. Looking at the ave() code, I can understand that choice:
function (x, ..., FUN = mean)
{
if (missing(...))
x[] <- FUN(x)
else {
g <- interaction(...)
split(x, g) <- lapply(split(x, g), FUN)
}
x
}
If the factor is missing an element, then the corresponding element of X
is not changed in the output:
fact <- gl(2,2)
fact[3] <- NA
fact
[1] 1 1 <NA> 2
Levels: 1 2
ave(1:4, fact)
[1] 1.5 1.5 3.0 4.0
That's a reasonable plan, but it isn't the documented functioning of
ave(). From the document...
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/ave.html
...you get next to nothing about what the function actually does. It
does say that x is "a numeric," but the function does not throw an error
when x is not numeric. So if someone writes code expecting numeric x,
but a user provides a non-numeric x, there may be trouble.
I suspect that the programmer saw that the code worked in her examples
and she went on to other things. I can't blame the documentation for
that, but it is possible that if it said something about the relation
between the type of the input and the type of the output she might have
written it differently. In addition, I probably would have caught it
sooner and I would have understood the problem.
This is how I'll recommend they fix the bug in the code (thanks to those
of you who helped with this):
temp.vec <- as.character( test.dat$FAMID[ test.dat$FTYPE != 6 ] )
test.dat$famsize[ test.dat$FTYPE != 6 ] <- as.vector( table( temp.vec )[
temp.vec ] )
rm(temp.vec)
I think we should force FAMID to be character from the beginning, though.
Best,
Mike
FYI -- RFGLS code that fails in RFGLS version 1.1:
library(RFGLS)
data(pheno)
data(geno)
data(map)
data(pedigree)
data(rescovmtx)
#comment out the following two lines and it will run correctly
pedigree$FAMID <- as.character(pedigree$FAMID)
pheno$FAMID <- as.character(pheno$FAMID)
minigwas <- gls.batch(phenfile=pheno,genfile=data.frame(t(geno)),
pedifile=pedigree,
snp.names=map[,2],input.mode=c(1,2,3),pediheader=FALSE,
pedicolname=c("FAMID","ID","PID","MID","SEX"),
phen="Zscore",covars="IsFemale",
outfile=NULL,col.names=TRUE,return.value=TRUE)
str(minigwas)
Mike
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