Description

Credential signals of biological origin in metabolomics data.

Installation

install.packages(“devtools”)
library(devtools)
install_github(“pattilab/credential”)

Example

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.

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.

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), 9583-95892014
doi:10.1021/ac503092d