In ericscrum/snpltools: Tools for the SNAPL Lab

knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)

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Introduction

• Background and Rationale
  • Why?
  • For whom?
  • What's the rationale?
• Objectives
  • What are we trying to establish?
  • What's the null result? Is that a stopping point?
  • What result is a success?

Data and Methods

• Data Desciption
  • That is the type of data?
  • Where did it come from?
  • How many samples?
  • Measurements per sample?
  • What are the covariates?
• Statistical and Analytical Methods
  • How will the data be processed?
  • Describe the analytical pipeline
  • What statistical tests will we employ?
  • How will we adjust for multiple testing
  • If the data will be filtered, what cut-offs will be used?

Results

• Summary of findings
  • Our interpretation
• Reference figures and tables, don't include in summary above
• List which files were produced and what they contain (eg. where the results are stored)

Conclusions

• For each objective in the introduction, did we meet that objective?
  • Why?
  • Do this in the order the goals are introduced
• Discuss the results of each test in the order the tests are described
• Do the findings make sense?
• What are some issues (eg. data qulity, caveats, limitations, etc.)

Keep in mind: report should be in prose $\leq 2$ pages

Sample Table

library(knitr)
kable(head(mtcars))

• What are some key values to notice?

Sample Plot

library(ggplot2)
ggplot(data = mtcars, aes(x = mpg, y = hp, colour = wt)) + geom_point() + geom_smooth(method = 'loess')

• What should this plot look like if there is no signal?
• What does this plot show?

Session information is saved to _r033-session-info.txt

writeLines(capture.output(sessionInfo()), "r03-session-info.txt")

ericscrum/snpltools documentation built on May 9, 2019, 5:24 p.m.