Washington University in St. Louis

The Patti Lab
Metabolomics to elucidate novel biochemical mechanisms of disease
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Job opportunities are available.

Credential Features

R Package

Feature credentialing can be downloaded as an R package from our github repository pattilab/credential.

Credentialing depends on several R packages. XCMS and CAMERA are available on Bioconductor.

Installation

install.packages("devtools")
library(devtools)

install_github("pattilab/credential")

Example

An example from the inst/ directory is shown here.

library(credential)

credentialed_features = credential(
  xs_a = xcms_set_a, 
  r_12t13_a = 3/4,
  an_a = xs_annotate_b, 
  
  xs_b = xcms_set_b, 
  r_12t13_b = 4/3,
  an_b = xsannoate_b, 
  
  isotope_rt_delta_s = 5,
  ppm_for_isotopes = 5,
  
  
  mixed_ratio_factor = 4,
  mixed_ratio_ratio_factor = 1.8
)

The output will include: credential_summary.txt - A count of features during each step of the credentialing process. credentialed_features.csv - The final credentialed features.

Comments

We are working to improve the process, if you have suggestions or would like us to implement a feature please contact us.

Mahieu NG, Huang X, Chen Y-J, Patti GJ
Credentialed Features: A Platform to Benchmark and Optimize Untargeted Metabolomic Methods
Anal. Chem., 86(19), 9583-9589, 2014
doi:10.1021/ac503092d

Washington University, Departments of Chemistry, Genetics, and Medicine. Saint Louis, Missouri 63110 USA