lookupTable: generates 'lookupTable' for filtering raw data post gene...

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

Description

returns three tables, 1. gene centric assembly readOrigin identities, 2. homologySearch assignment, 3 superimposed

Usage

lookupTable(genesOfInterest = scg,
  annotations = "~/simulation_fr_the_beginning/out/template.csv", rs)

Arguments

genesOfInterest	the kos of interest defaults to scg must be in the ko:KXXXXX format
annotations	table containing the number of KOs for each taxID
rs	processed readStatuses from newbler output

Examples

## Not run: 
anno = "~/simulation_fr_the_beginning/out/template.csv"
rs = lapply(dynList, function(x) x$rs %>% mutate(ko = x$ko)) %>%
   do.call(rbind,.)
output = lookupTable(genesOfInterest = scg,
   annotations = anno, rs)
e

## End(Not run)

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