Help for SeqVarData function
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pjuge • 0
@bcf8f511
Last seen 12 months ago
United States

Hi everyone,

I am having a coding problem while using SeqVarData function. I believe I've been using the same exact code with the same type of data and it worked perfectly so I don't know what I' doing wrong this time.

Here is the code I'm running:

seqData <- SeqVarData(gds, sampleData=annot)

And here is the error message:

Error in (function (cond) : error in evaluating the argument 'data' in selecting a method for function 'AnnotatedDataFrame': is.character(gdsfile) | inherits(gdsfile, "SeqVarGDSClass") is not TRUE

When I run

is.character(gdsfile) 

[1] TRUE

or

inherits(gdsfile, "SeqVarGDSClass")

[1] FALSE

If someone had an idea of what the problem may be, that would be super helpful! Thanks a lot!

Biobase SeqVarTools • 846 views
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Entering edit mode

In your first block of code, the object is called 'gds', but in the second and third blocks it's called 'gdsfile'. Presumably those aren't the same things?

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Entering edit mode

Sorry my mistake,

With the correct input

is.character(gds) > FALSE

inherits(gds, "SeqVarGDSClass") > TRUE

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Entering edit mode
@stephanie-m-gogarten-5121
Last seen 4 months ago
University of Washington

I think you might have mixed up your objects, because the error message makes no sense to me. An AnnotatedDataFrame method should not be operating on a GDS object. Try restarting your R session and starting over, and if you still get an error, provide all your code (not just the last line) and the output of sessionInfo().

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I restarted my R session, opened a new project and it worked! I don't know what I did, but I guess I am relieved it's working now... Thank you for your help :)

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