btESBL_contigclusters_msa_blastoutput: Data: Contig clusters BLASTed against ISFinder,...
In joelewis101/blantyreESBL: Data and Code Repository For a Study Describing Antimicrobial Resistance in Blantyre, Malawi
btESBL_contigclusters_msa_blastoutput R Documentation
Data: Contig clusters BLASTed against ISFinder, PLasmidFinder, SRST2 databases
Description
Outputs of BLASTing contig cluster representative cluster agains the ISFinder
PlasmidFinder and SRST2 databases.
Usage
btESBL_contigclusters_msa_blastoutput
Format
A named list of ten data frames, where name is cluster id. Columns are:
- qseqid
Query sequence name
- sseqid
Source (ie. database) sequence name
- sseqid_group
Source gene family if IS/SRST2
- sseqid_gene
Source gene if IS/SRST2
- pident
Sequence identfity of query
- slen
Source gene length
- length
Length of match of query
- qstart
Query match start coordinate
- qend
Query end match coordinate
- sstart
Source match start coordinate
- send
Source end match coordinate
- evalue
BLAST e value of match
- bitscore
BLAST bitscore of match
- type
Type of database used: amr,is, plasmid
joelewis101/blantyreESBL documentation built on Nov. 1, 2023, 1:43 p.m.
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| btESBL_contigclusters_msa_blastoutput | R Documentation |
Data: Contig clusters BLASTed against ISFinder, PLasmidFinder, SRST2 databases
Description
Outputs of BLASTing contig cluster representative cluster agains the ISFinder PlasmidFinder and SRST2 databases.
Usage
btESBL_contigclusters_msa_blastoutput
Format
A named list of ten data frames, where name is cluster id. Columns are:
- qseqid
Query sequence name
- sseqid
Source (ie. database) sequence name
- sseqid_group
Source gene family if IS/SRST2
- sseqid_gene
Source gene if IS/SRST2
- pident
Sequence identfity of query
- slen
Source gene length
- length
Length of match of query
- qstart
Query match start coordinate
- qend
Query end match coordinate
- sstart
Source match start coordinate
- send
Source end match coordinate
- evalue
BLAST e value of match
- bitscore
BLAST bitscore of match
- type
Type of database used: amr,is, plasmid
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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