View source: R/read.blast6out.R
read.blast6out | R Documentation |
Read a file in blast6out format generated by either USEARCH or VSEARCH.
read.blast6out(blast6out.file)
blast6out.file |
to blast6out file ( |
A dataframe storing the following columns:
query:
query id.
subject:
subject id.
perc_ident:
pecent identity between query and subject.
align_len:
alignment length between query and subject.
n_mismatch:
number of mismathces between query and subject.
n_gap_open:
number of gap openings between query and subject.
start_q:
start position in query. Query coordinates start with 1 at the
first base in the sequence as it appears in the input file. For translated searches (nucleotide queries, protein targets), query start < end for +ve frame and start > end for -ve frame.
end_q:
end position in query.
start_s:
start position in subject. Subject coordinates start with 1 at
the first base in the sequence as it appears in the database. For untranslated
nucleotide searches, subject start < end for plus strand, start > end for a reverse-complement alignment.
end_s:
end position in subject.
evalue:
evalue calculated using Karlin-Altschul statistics.
bit_score:
bit score calculated using Karlin-Altschul statistics.
Hajk-Georg Drost
# read example *.blast6out file test.blast6out <- read.blast6out(system.file("test.blast6out", package = "LTRpred")) # look at the format in R head(test.blast6out)
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