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yanglab-computationalgenomics / Starfish

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starfish_link function error #2

Open seqyuan opened 2 years ago

seqyuan commented 2 years ago

example_sv was used to test Starfish, Here is my test command: starfish_link_out = starfish_link(example_sv, prefix = "example") I got the following error:

Evaluating the statistical criteria
Successfully finished!
Running..

Evaluating the statistical criteria
Successfully finished!
Error in .(chr) : could not find function "."
In addition: There were 50 or more warnings (use warnings() to see the first 50)
seqyuan commented 2 years ago

when I changed starfish_link.r line 152 from svtra <- plyr::ddply(svtra, .(chr), transform, n = length(chr)) to svtra <- plyr::ddply(svtra, "chr", transform, n = length(chr))

lsbaoouc commented 2 years ago

when I changed starfish_link.r line 152 from svtra <- plyr::ddply(svtra, .(chr), transform, n = length(chr)) to svtra <- plyr::ddply(svtra, "chr", transform, n = length(chr))

Hi seqyuan,

Please check the tutorial and make sure you have loaded all the required packages. Specifically, you need plyr (1.8.6) to use the function. Please let me know if you still get the problem after that.

Lisui