load_hittable | R Documentation |
This must be a TAB-delimited file with a header and the following columns:
load_hittable(filename, na_str = "N/A")
filename |
Filename or URL. This will be read by
|
na_str |
The characters that indicate missing data. NCBI-blast uses 'N/A', so that is the default here. |
qseqid - an identifier for the query sequence
evalue - the e-value reported by BLAST
score - the raw score (not the bitscore)
staxid - the subject taxon
A data.frame
The staxid column must contain NCBI taxon ids. One hit may be associated with multiple taxon ids. In this case, we assume that all other fields are the same over the row, and create one new row for each taxa. This situation occurs, for example, in RefSeq databases, where identical sequences that are shared between multiple taxa are merged into one.
If any entries are missing taxon ids, then a warning is raised. If there are only a few missing ids, this may be fine. For example, some entries in RefSeq have no associated taxon ID. But if most or all of the ids are missing, then you probably need to reformat your BLAST database with a taxon table.
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