R error : "attempt to select less than one element in get1index"

Question

I'm a beginner in R and I'm trying to use the package ClonEvol, however the documentation on the github webpage is very limited. So for now I'm using their example code and trying to adapt it to my data called ce.

  ce <- data.frame(
  cluster = c(1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,6,6,6,6,7,7,7,7),
  gene = c("geneA","geneB","geneC","geneD","geneA","geneB","geneC","geneD","geneA","geneB","geneC","geneD","geneA","geneB","geneC",
 "geneD","geneA","geneB","geneC","geneD","geneA","geneB","geneC","geneD","geneA","geneB","geneC","geneD"),
  prim.vaf = c(0.5,0,0,0,0.5,0.5,0,0,1,0.5,0,0,1,0.5,0,0.5,0.5,0.5,0,0.5,0.5,0.5,0,1,0.5,0.5,0.5,0)
        )

    cluster <- ce$cluster
    gene <- ce$gene
    prim.vaf <- ce$prim.vaf

    x <- ce

    vaf.col.names <- grep('prim.vaf', colnames(x), value=T)
    sample.names <- gsub('prim.vaf', '', vaf.col.names)
    x[, sample.names] <- x[, vaf.col.names]
    vaf.col.names <- sample.names
    sample.groups <- c('P', 'R');
    names(sample.groups) <- vaf.col.names
    x <- x[order(x$cluster),]

    pdf('box.pdf', width = 3, height = 5, useDingbats = FALSE, title='')
    pp <- variant.box.plot(x,
   cluster.col.name = ce$cluster,
   show.cluster.size = FALSE,
   cluster.size.text.color = 'blue',
   vaf.col.names = vaf.col.names,
   vaf.limits = 70,
   sample.title.size = 20,
   violin = FALSE,
   box = FALSE,
   jitter = TRUE,
   jitter.shape = 1,
   jitter.color = clone.colors,
   jitter.size = 3,
   jitter.alpha = 1,
   jitter.center.method = 'median',
   jitter.center.size = 1,
   jitter.center.color = 'darkgray',
   jitter.center.display.value = 'none',
   highlight = 'is.driver',
   highlight.note.col.name = 'gene',
   highlight.note.size = 2,
   highlight.shape =16,
   order.by.total.vaf = FALSE
    )
    dev.off()

However, I get the following error :

    Error in .subset2(x, i, exact = exact) : recursive indexing failed at level 2

And if I delete cluster.col.name=ce$cluster and vaf.col.names=vaf.col.names, the error becomes the following :

    Error in .subset2(x, i, exact = exact) : attempt to select less than one     
    element in get1index

Has someone any idea of what went wrong ?

Answer 1

I met this error message today. I know little about the R package in this question, but I think I can show what the error message means here. And maybe it is useful for you to find out the problem.

The error occurs when we use NULL as an index to subset a list.
Here are the expressions invoking this error message:

any.list <- list(1, 2, 3)
# If single brackets, no error occurs: 
any.list[NULL]
## list()

# If double brackets, the error occurs: 
any.list[[NULL]]
## Error in any.list[[NULL]] : 
##   attempt to select less than one element in get1index

The list above can be any list, or even a vector.

a.vector <- c(1, 2, 3)
a.vector[[NULL]]
## Error in a.vector[[NULL]] : 
##   attempt to select less than one element in get1index

Here is a similar error message:

any.list[[0]]
## Error in any.list[[0]] : 
##   attempt to select less than one element in get1index <real>

END