phyleria / getSpecificTaxId

A package with a function that imports data from BugSigDB using bugSigdbr and returns Signatures with a specified Tax. Id

getSpecificTaxId Package

The goal of the getSpecificTaxId package is to allow the access of specific Tax Ids without extracting all the Ids available.

Installation

You can install the development version of packagetemplate from Github with:

install_github("getSpecificTaxId")

Example

This is a basic example which shows how to use getSpecificTaxId:

library(getSpecificTaxId)

getMetaphlan <- getSpecificTaxId(df,
                                 tax.id.type = ("metaphlan"),
                                 tax.level = "mixed",
                                 exact.tax.level = TRUE,
                                 min.size = 1)
#> $`bsdb:1/1/1_adenoma:conventional-adenoma-cases_vs_controls_UP`
#>  [1] "k__Bacteria|p__Firmicutes|c__Bacilli"                                                                                        
#>  [2] "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria"                                                                        
                                                          
#> 
#> $`bsdb:1/1/2_adenoma:conventional-adenoma-cases_vs_controls_DOWN`
#> [1] "k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus"
#> [2] "k__Bacteria|p__Cyanobacteria"                                                                            
#> 
#> $`bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP`
#> [1] "k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes"                                 
#> [2] "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae"