[R] Error in inherits(x, "data.frame") : subscript out of bounds
Uwe Ligges
ligges at statistik.tu-dortmund.de
Sun Mar 7 19:45:10 CET 2010
On 05.03.2010 15:24, kloytyno at mappi.helsinki.fi wrote:
> Hi,
> I have a list p with different size dataframes and length of over 8000.
> I'm trying to
> calculate correlations between the rows of dataframes of this list and
> columns of another
> dataset (type data.frame also) so that first column is correlated with
> all the rows in
> the list dataframe. Some information from another dataset is also
> included to the final
> output (all.corrs). This worked a couple of weeks ago when I wrote it
> but now it seems
> not to, and gives an error message:
>
> Error in inherits(x, "data.frame") : subscript out of bounds
> In addition: There were 50 or more warnings (use warnings() to see the
> first 50)
> warnings()
> Warning messages: 1: In corrs[j] <- cbind(expressions[j, 1:5],
> SNP.expr.cor) :
> number of items to replace is not a multiple of replacement length
>
> which indicates that the problem is with getting correlation and other
> information into
> corrs. cbind(expressions[j,1:5], SNP.expr.cor) is type data.frame.
> Changing corrs into
> matrix, dataframe, list or any other type has not helped.
>
> I've updated R from 2.9.0 to the recent version in between. Would anyone
> have a solution
> for this problem? I very much appreciate all help.
>
> SNP.expr.cor<-NULL
> all.corrs<-NULL
> corrs<-NULL
>
> for(i in 1:length(p)){
> dim.exp<-dim(p[[i]])
> expressions<-p[[i]]
> expressions.m<-as.matrix(expressions[,6:48])
> for(j in
> 1:dim.exp[1]){
> SNP.expr.cor<-cor(genotypes[,i],expressions.m[j,],use="na.or.complete")
> corrs[j]<-cbind(expressions[j,1:5], SNP.expr.cor)
> }
> all.corrs[i]<-list(cbind(map[i,1:6], corrs))
> }
>
>
> BR
> Katja
>
Your example is not reproducible, since we do not have the data. What I
guess is that you need to make your objects lists in advance. I cannot
try out, but maybe the following works better right away
all.corrs <- vector(mode = "list", length = length(p))
for(i in seq(along = p)){
dim.exp <- dim(p[[i]])
corrs <- vector(mode = "list", length = dim.exp[1])
expressions <- p[[i]]
expressions.m <- as.matrix(expressions[,6:48])
for(j in 1:dim.exp[1]){
SNP.expr.cor <- cor(genotypes[, i], expressions.m[j, ], use =
"na.or.complete")
corrs[[j]] <- cbind(expressions[j, 1:5], SNP.expr.cor)
}
all.corrs[[i]] <- list(cbind(map[i, 1:6]), corrs)
}
Best,
Uwe Ligges
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