haotu : an open lab notebook

2014/11/07

BLAST from R

Filed under: Uncategorized — Tags: , , , , , , — S @ 08:16

There is a nice post here on the topic
The post takes code from the blastSequences function in the R package annotate

However, the code does give an object with enough info to then retrieve the sequences. I edited this code to be able to perform BLASTs in R for a given organism filter. The returned object gives gene ids and definitions.

You can find my cleaned and edited code is here

Error in write.table because data.frame contains a list

Filed under: Uncategorized — Tags: , , , — S @ 06:42

Error in .External2(C_writetable, x, file, nrow(x), p, rnames, sep, eol, :
unimplemented type 'list' in 'EncodeElement'

I got this error when trying to write a table write.table on an object. The object was a data.frame but one of the elements was a list (it is unclear why it was a list, just R magic). The simplest workaround is to convert the data.frame to a matrix as.matrix and save that object with write.table

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