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"

getspecifictaxid's Issues

Feedback

Hi @phyleria,

Thanks for this contribution. Since it's not required to know R or Bioconductor Packages for this project, I'm mostly looking for attention to detail in this contribution task.

Very neat work. Although the function doesn't work because sigs isn't defined, I can see how neatly you write code. Regarding your vignette, I think you could have unified the code block so that lines 17-18 could be with your examples. As it is, text in lines 20-28 are part of the code block. I had also requested as part of step 4 that you update the DESCRIPTION file.