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.
install.packages("devtools") library(devtools) install_github("pattilab/credential")
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.
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