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), 9583-9589, 2014
doi:10.1021/ac503092d