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L1KProcs: an R package for L1000 data processing and analysis

L1KProcs: an R package for L1000 data processing and analysis. Chenglin Liu , Kun Wei and Jing Su Center for Bioinformatics and Systems Biology Wake Forest School of Medicine. Overview. L1KProcs.

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L1KProcs: an R package for L1000 data processing and analysis

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  1. L1KProcs: an R package for L1000 data processing and analysis Chenglin Liu , Kun Wei and Jing Su Center for Bioinformatics and Systems Biology Wake Forest School of Medicine

  2. Overview

  3. L1KProcs • L1KProcs is an R package and interface for LINCS L1000 data preprocessing and compound signature detection in both text-mode and graphic-mode way. • Additionally, it is a library for existing L1000 processed expression data and their connections (EGEM library).

  4. L1KProcs • Operating system: • Windows XP, Windows 7, Linux, Mac OS X • Open source • R language based (R>=3.0) • Parallel computing • Require doParallel package • Access • download, web

  5. Function I: preprocessing

  6. How to Use • Required Input: the location of raw L1000 data • Optional Input: • target: quantile normalization • ifAll: if convert the landmark gene expression to whole genome data • nthread: number of parallel computing • plot: data quality visualization • Output: • The processed data saved in outpath. • The information of the data including the qualities and the control wells in class listlstPlateInfo.

  7. data quality visualization

  8. Single well peak calling and visualization

  9. Function II: EGEM matrix • Required Input • cpdata: LFC after compound treatments • Optional Input • LINCS: • if TRUE, specify the name of the existing EGEM library lib.name • otherwise, provide the LFC after knockdown treatments • nthread: number of parallel computing • Output • The EGEM matrix and annotations

  10. Function II: EGEM matrix

  11. Function III: Compound Signature Discovery • Required Input • The output of Function II egem.info. • The range of signature number pNo. • Optional Input • nthread: number of parallel computing • Output: • Signature number k • Compounds and signature genes.

  12. Function III: Compound Signature Discovery

  13. L1KProcs Interface

  14. L1000 preprocessing Choose one raw L1000 data Upload and start computing

  15. Compound Signature Discovery nthread • start computing

  16. Single well peak calling visualization

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