readat: An R package for reading and working with SomaLogic ADAT files

Richard J Cotton; Johannes Graumann

doi:10.1186/s12859-016-1007-8

readat: An R package for reading and working with SomaLogic ADAT files

BMC Bioinformatics. 2016 May 4;17(1):201. doi: 10.1186/s12859-016-1007-8.

Authors

Richard J Cotton¹, Johannes Graumann²

Affiliations

¹ Proteomics Core, Weill Cornell Medicine - Qatar, PO Box 24144, Doha, State of Qatar.
² Proteomics Core, Weill Cornell Medicine - Qatar, PO Box 24144, Doha, State of Qatar. jog2030@qatar-med.cornell.edu.

Abstract

Background: SomaLogic's SOMAscan™ assay platform allows the analysis of the relative abundance of over 1300 proteins directly from biological matrices such as blood plasma and serum. The data resulting from the assay is provided in a proprietary text-based format not easily imported into R.

Results: readat is an R package for working with the SomaLogic ADAT file format. It provides functionality for importing, transforming and annotating data from these files. The package is free, open source, and available on Bioconductor and Bitbucket.

Conclusions: readat integrates into both Bioconductor and traditional R workflows, rendering it easy to make use of ADAT files.

Keywords: ADAT; Bioconductor; Dynamic range; Proteomics; R; Software; SomaLogic.

Publication types

Evaluation Study

MeSH terms

Adult
Aged
Chorionic Gonadotropin / blood*
Cohort Studies
Cross-Sectional Studies
Female
Follicle Stimulating Hormone / blood*
Humans
Internet
Male
Middle Aged
Prostate-Specific Antigen / blood*
Proteomics / methods*
Software

Substances

Chorionic Gonadotropin
Follicle Stimulating Hormone
Prostate-Specific Antigen