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MetamapsDB

R package for querying integrated -omics database.

Introduction

MetamapsDB is a R package used for interfacing with such a database for

Gene centric queries
Analyses of Integrated^ Microbiome datasets

^ Genomic and Transcriptomic

It is the final step of the 5 preprocessing steps used in carrying out our gene centric pipeline. (Unpublished)

Annotation DIAMOND - Labelling of short reads using, blastX-like against NR protein database (more for functional)
Binning MEGAN6 CE - Functional (KEGG) binning of NGS short reads based on labels
Bin-based Assembly NEWBLER - Gene Centric OLC Assembly of functional bins / KEGG Orthologs
- Annotation DIAMOND - Labelling (round2) more for taxonomic annotation
- MEGAN6 CE - Taxonomic binning of contigs based on labels
Gene centric analyses pAss -
- Identify Maximum Diversity Region (MDR)
- Remove known KOs which fail process
  - Diversity analysis (gene count)
    - 31 Single Copy Genes
  - ID genera which are indistinguishable due to sequence conservation
mapBlat - Maps (using BLAT) gDNA and rRNA short onto
- the contigs
- just the MDR Region

Mentioned Packages

OMICS

Docker wrapper for generating a KEGG + Taxnoomy + Contig neo4j graph database

MapBloat

R package for mapping reads onto contigs/MDR using Blat

Usage

Functions

Function	Description
connect	Connects with Neo4J database
dbquery	Sends query to Neo4J database
koname	Takes ko id as input and returns ko details
taxnam.sql	Takes NCBI taxonomy id as input and returns ko details
contractMetab	Simplifies KEGG metabolic graph
igraph2gexf	Encodes Igraph into gexf format
sigmaGraph	Generates an interactive graph representation of a subnetwork in html using the `htmlwidgets` package
grepgraph	given a set of KOs get the subgrap of metabolism
grepgraph.cpd	given a set of CPDs get the subgrap of metabolism
annotateContigs.taxonomy
buildE
buildTree
extractFromPath
findK
findSeeds
findTrios
findtype
getContigs
gi2rank
ig2ggvis
ksCal
lca
make.data.frame	Utily function dbquery might return data.frame where each column is a nested list. Converts lilst to dataframe
trio
trio.local

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Version

Install

install.packages('MetamapsDB')

Monthly Downloads

4

Version

0.0.2

License

GPL (>= 2)

Maintainer

Wesley GOI

Last Published

December 6th, 2017

Functions in MetamapsDB (0.0.2)

annotateContigs.taxonomy

Adds taxonomic annotations of the contigs

dynPlot Diagnostic plots

Given a igraph object, adjacentPairs finds adjacent pairs of KOs

Find all trios surrounding the KO of interest

dynamicThreshold

dynamicThreshold tries to identify the lower bound converage value in order to remove low quality contigs. Number of contigs tend to stablize at a value when removing reads below a certain readnum and we try to identify the min read required for that region of stability

Connecting to NEO4J Graph Database.

addContigProperty

addContigProperty

contigsSurvive.repeats.readNum

contigsSurvive.repeats.readNum

buildE sorts the tree into a data.frame

with Pipe operator

Taxonomic tree of the taxons

Double Pipe operator

extractFromPath

extractFromPath

searches for KO's homology assignments

contigsSurvive.repeats.rpk

contigsSurvive.repeats.rpk

Returns the metabolic graph given vector of KOs

contractMetab shrinks a metabolic network's KOs into non-redundant units

Returns the metabolic graph given vector of KOs

Finds the details of the CPD when given its ID

findK to find the optimum number of Ks

Function for querying metamaps DB

ko2path Finds all pathways related to the KO Finds all associated pathways, and returns a data.frame with ko and pathway details

findV finds the vertixID in the graph given its name

finds the location of the MDR on the contig

findType finds KOs/compounds ID in metabolic graph

Converts igraph obj two gexf Function for converting igraph 2 gexf

returns metabolic graph with all the ornaments set Adds details into the igraph object

Indexes the database for faster retrieval

mappingInfo sequence analysis of contigs (for SIMULATION only)

grepReads greps for cDNA or gDNA reads cause they are both grouped togehter in the assembly input

Returns contig ranges for those captured within the MDR

make.data.frame

Convert columns with nested list structures into plain vectors

Finds all KOs in a given pathway Finds all KOs belonging to a Pathways

map takes cDNA reads (fastQ format) and maps them onto contigs

findPerl finds the path to the executable

List Pathways Lists all metabolic pathways

findPython finds the path to the executable

Convert igraph to ggplot2 object

Generates metabolic network as IGRAPH object from input vector KOs Returns the metabolic graph given vector of KOs

Function for querying metamaps DB

List all intermediaries between taxa and the superkingdom it belongs to

generates `lookupTable` for filtering raw data post gene centric assembly

readStatusReader

readStatusReader stores read assignment details from the simulation and assigns the contig a genome of origin

plotClassification

Plot clustering

Lists the taxonomic id's details

finds all simulated genera for that particular KO

singleCopyGenes'

Gives KO details when supplied with KO id

To find all seed compounds in the metabolic graph

findTrios searches valid three-KO reactions resticting by the center KO and reports reaction clusters

ksCal generates KS statistics for aKO given the base distribution

Finds the lowest common ancestor

rolling A dynamic threshold for the killing redundant contigs

surrNODES finds nodes which are surrounding the given node