Question

Error: no slot of name "start" for this object of class "XStringViews"

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jbtouching • 0

@jbtouching-9798

Last seen 8.1 years ago

I was running a function:

doCimplAnalysis(data = idata, scales = scale, n_iterations = 1, BSgenome = Hsapiens, system = "SB", verbose = FALSE)

However, I encountered a error that I am not sure about:

"Error in FUN(X[[i]], ...) : no slot of name "start" for this object of class "XStringViews" Called from: FUN(X[[i]], ...) "

I have done some searching. I found that the new "XStringViews" has no the slot name, start, but the "XStringViews" of older version might have this slot name. It seems that the slot name, start, is required for doCimplAnalysis function. Thus, I would like to consult to get around this problem.

Thanks a lot !

XStringViews biostrings • 1.4k views

ADD COMMENT • link 8.2 years ago • updated 8.1 years ago jbtouching • 0

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When you post a question please include a few lines of code that reproduce the problem (ie, code that others can run and see the error you're getting). Also show the output of sessionInfo() so we can see what package versions you're using.

If you suspect old package versions you can update with biocLite(). If you think there's a problem with doCimplAnalysis() you should tag your question with the package name to draw the attention of the author.

Valerie

ADD REPLY • link 8.2 years ago Valerie Obenchain ★ 6.8k

score 0 · Answer 1 · 2016-03-28

Thanks for the response.

The packages used several sources that I cannot paste them all.

However, I have checked the codes and found the problem is related to the following codes :

function(chr) {
if (verbose) cat(paste('>>>> chromosome', chr, '<<<<\n'))

       if ( specificity.pattern != '' ) {
           strReverse <- function(x) sapply(lapply(strsplit(x, NULL), rev), paste, collapse="")
           background <- c(matchPattern(specificity.pattern, BSgenome[[chr]])@start, matchPattern(strReverse(specificity.pattern), BSgenome[[chr]])@start)
       } else {
           background <- NULL
       }

}

## errors update:

##Error in matchPattern(specificity.pattern, BSgenome[[chr]]) :
## error in evaluating the argument 'subject' in selecting a method for function 'matchPattern': Error in BSgenome[[chr]] : no such sequence