| readHmmer {micropan} | R Documentation |
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 |
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. |
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.
Value
The results are returned in a ‘tibble’ with columns ‘Query’, ‘Hit’, ‘Evalue’, ‘Score’, ‘Start’, ‘Stop’ and ‘Description’. ‘Query’ is the tag identifying each query sequence. ‘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.
Author(s)
Lars Snipen and Kristian Hovde Liland.
See Also
hmmerScan, hmmerCleanOverlap, dClust.
Examples
# See the examples in the Help-files for dClust and hmmerScan.