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| RE: How to extract the species vectors from the BOLD sequences? [ Reply ] By: Samuel Brown on 2012-03-18 23:06 | [forum:5591] |
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Hi Sergey In addition to the method suggested by Rupert, you can use the attr(object, "species") function to retrieve the species vector: nn <- search.BOLD("Dolomedes") tt <- read.BOLD(nn) str(tt) #Investigate the structure of the object spp <- attr(tt, "species") spp |
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| RE: How to extract the species vectors from the BOLD sequences? [ Reply ] By: Rupert Collins on 2012-03-18 22:31 | [forum:5590] |
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Hi Sergey. Thanks for posting. We've very recently updated the BOLD search function, and a new version on Spider (1.1-2) is up on CRAN. I recommend you install it, as the previous version no longer works. #get newest Spider version install.packages("spider") Now, you can try this example to get the species vectors from BOLD data. You need to split the taxon labels at the pipe symbol. #seach BOLD for genus "Dolomedes" nn <- search.BOLD("Dolomedes") #download DNA seqs from BOLD tt <- read.BOLD(nn) #split the taxon labels at the pipe spp <- strsplit(names(tt), split="\\|") #grab the second element as the species vector spp <- sapply(spp, function(x) x[2]) Hope this helps. Rupert |
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| How to extract the species vectors from the BOLD sequences? [ Reply ] By: Sergey Turanov on 2012-03-17 12:20 | [forum:5588] |
| I still have not understood how to do it. Help, please. | |
