contigInfo: contigInfo

In MetamapsDB: Network Analysis of Metabolic Pathways and Gene Based Assemblies in Metagenomics

Description

contigInfo function greps the contig related info such as whether its in the MDR

Usage

contigInfo(ko, contig, withAnnotation = FALSE)

Arguments

ko	the ko bin which the contig was assembled from
contig	contigID (optional)
withAnnotation	0j/

Examples

## Not run: 
To query a specific contig
contigInfo(ko = "K00001", contig="contig00001")
# Sending query
# Query Completed

#        bin             contig MDR spanning readnum length
#1 ko:K00001 K00001:contig00001   1        1    1497   1236
With annotation
   assignment taxid       bin             contig readnum length MDR spanning
1 Bacteroides   816 ko:K00001 K00001:contig00001    1497   1236   1        1
2 Bacteroides   816 ko:K00001 K00001:contig00001    1497   1236   1        1
     Rank
1   genus
2 simTaxa

To query all contigs associated with a KO
contigInfo(ko = "K00001") %>% head
#Sending query
#
#Query Completed
#
#   MDR spanning       bin             contig length readnum
#1 <NA>     <NA> ko:K00001 K00001:contig00168    297      31
#2 <NA>     <NA> ko:K00001 K00001:contig00167    298     118
#3    1        0 ko:K00001 K00001:contig00166    298      45
#4    1        0 ko:K00001 K00001:contig00164    299     236
#5    1        1 ko:K00001 K00001:contig00163    300     106
#6 <NA>     <NA> ko:K00001 K00001:contig00162    302     310

## End(Not run)

MetamapsDB documentation built on May 1, 2019, 9:23 p.m.