Generating reports. Steffen Durinck

Transcription

1 Generating reports Steffen Durinck

2 Traditional way of writing Analyze the data reports Copy results of the analysis in a report Copy results from report into paper to submit

3 Workflow

4 Report Easy to update analysis Contain R analysis code Dynamic pdf format

5 Workflow

6 Report Easy to update analysis Contain R analysis code Dynamic pdf format Reproducable

7 Forensic bioinformatics Keith Baggerley recent talk coined term Forensic Bioinformatics Try to reconstruct the analysis that was actually performed What the methods section in the paper says that has been done

8 Example Genomic signatures to guide the use of chemotherapeutics Potti et al., Nature Medicine - 12, (2006) Microarrays: retracing steps - pp Kevin R Coombes, Jing Wang & Keith A Baggerly This week s Nature Medicine

9 Example NCI60 cell lines Drug response data Microarray expression data Use NCI60 expression data to find set of genes that can be used as predictor for treatment outcome in cancer tumors

10 Example Recent studies have suggested how this approach might work using a widely-used panel of cell lines, the NCI60, to assemble the response signatures for several drugs. Unfortunately, ambiguities associated with analyzing the data have made these results difficult to reproduce. Keith Baggerly - Mathematical Systems Biology of Cancer II talk

11 Example Prediction on other samples worked using their software But same gene set could also predict outcome for other drugs???? Keith Baggerly - Mathematical Systems Biology of Cancer II talk

12 Forensic bioinformatics: investigation results Gene signature was offset by 1 -> indexing error Training of algorithm was performed on training + test set => Near perfect prediction results Keith Baggerly - Mathematical Systems Biology of Cancer II talk

13 Sweave Developed by Friedrich Leisch A tool that allows Embedding of R code in LaTeX documents Code, results and descriptions are presented in a consistent way

14 Sweave Tables, graphs generated on the fly Dynamic reports which can be updated automatically

15 Sweave - how it works Write mix of LaTeX code and R code in.rnw file Run Sweave function in R on the created.rnw Run latex on the created.tex file

16 Rnw example \documentclass[11pt]{article} \usepackage{hyperref} \usepackage{url} \usepackage[authoryear,round]{natbib} \newcommand{\rfunction}[1]{{\texttt{#1}}} \newcommand{\robject}[1]{{\texttt{#1}}} \newcommand{\rpackage}[1]{{\textit{#1}}} \author{steffen \begin{document} \title{phd course Copenhagen} \maketitle

17 Rnw example \section{selecting a BioMart database and dataset} \subsection{selecting a BioMart database} Every analysis with \Rpackage{biomaRt} starts with selecting a BioMart database to use. A first step is to check which BioMart web services are available. The function \Rfunction{listMarts} will display all available BioMart web services \begin{scriptsize} <<>>= library(biomart) \end{document}

18 Rnw example > Sweave( example.rnw ) % latex example.tex example.pdf

19 Rnw example

20 Rnw R-code enclosed in <<>>= R-code goes

21 Sweave options echo: eval: TRUE/FALSE To display code or not TRUE/FALSE To evaluate code or not

22 Sweave options fig: TRUE To plot and include images

23 Rnw Lets create a data object <<>>= a = Lets create a second object <<echo = FALSE>>= b =

24 Rnw Now some code we don t want to be evaluated <<eval=false>>= Lets make a plot <<fig=true>>= plot(a,b, pch=16, col= lightblue

25 tables Do the analysis <<>>= data(cats, package= MASS ) lmout = lm(hwt ~ Bwt * Sex, data = Create a table <<results = tex>>= library(xtable)

26 Report versions of used packages Output of analysis may depend on version of packages used. E.g. GO or annotation packages Report package vesion by including tolatex(sessioninfo()) in your report.

27 Stangle Extract R-code only from Rnw file > Stangle("rnw-example.Rnw") Writing to file rnw-example.r Code can then be sourced (and run) in R

28 Weaver Developed by Seth Falcon Caching of results Avoids having to re-compute a computationally intensive piece of code each time one changes the document

29 Weaver Usage: In Rnw file: <<cache = TRUE>> your code to Sweave( yourrnw.rnw, driver = weaver())

30 Weaver Note: No side effects (e.g. printing, plotting) will work in a cache = TRUE code chunk If change in code chunk is detected cache will be recomputed Cache is not document specific. Two documents with same piece of code in same directory will give same cache!

31 Compendia Combine data and data analysis in an R package Easy way to add to publication Can also be published on BioC site as example data analysis

32 Live demo

33 References