micropan (version 1.2)

readHmmer: Reading results from a HMMER3 scan

Description

Reading a text file produced by hmmerScan.

Usage

readHmmer(hmmer.file, e.value = 1, use.acc = TRUE)

Arguments

hmmer.file

The name of a hmmerScan result file.

e.value

Numeric threshold, hits with E-value above this are ignored (default is 1.0).

use.acc

Logical indicating if accession numbers should be used to identify the hits.

Value

The results are returned in a data.frame with columns Query, Hit, Evalue, Score, Start, Stop, Description. Query is the tag identifying each sequence in each genome, typically GID111_seq1, GID121_seq3, etc. Hit is the name or accession number for a pHMM in the database describing patterns. The Evalue is the ievalue in the HMMER3 terminology. The Score is the HMMER3 score for the match between Query and Hit. The Start and Stop are the positions within the Query where the Hit (pattern) starts and stops. Description is the description of the Hit.

There is one line for each hit.

Details

The function reads a text file produced by hmmerScan. By specifying a smaller e.value you filter out poorer hits, and fewer results are returned. The option use.acc should be turned off (FALSE) if you scan against your own database where accession numbers are lacking.

See Also

hmmerScan, hmmerCleanOverlap, dClust.

Examples

# NOT RUN {
# See the examples in the Help-files for dClust and hmmerScan.

# }