vignettes/data-vignette.md

In miepstei/MetabolonR: Loads, Manipulates on Metabolon Datasets

title: "How to Read and manuipulate Metabolon Data" author: "Michael Epstein" date: "2016-04-20" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Vignette Title} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

This is a short vignette documenting how to load and manuiplate Metabolon data in R.

Load data

First we shall load three data frames that represent the sample metadata, metabolite metadata and the raw metabolite counts for each metabolite in each sample:

data(metaboliteDataWide)
data(metaboliteInfo)
data(sampleInfo)

The sample metadata contains information about the sample names, sample volume and when each sample was run (vital for the median normalisation):

data(sampleInfo)
knitr::kable(head(sampleInfo[,c("SAMPLE_NAME","PARAM_SUBJECT_ID","PARAM_RUN_DAY","PARAM_VOLUME_EXTRACTED_UL")], 10))

|SAMPLE_NAME |PARAM_SUBJECT_ID | PARAM_RUN_DAY| PARAM_VOLUME_EXTRACTED_UL| |:-----------|:----------------|-------------:|-------------------------:| |METAB1 | | 1| NA| |METAB2 | | 2| NA| |METAB3 |PATIENT1 | 1| 95| |METAB4 |PATIENT1 | 1| 95| |METAB5 |PATIENT1 | 1| 95| |METAB6 |PATIENT1 | 1| 95| |METAB7 |PATIENT1 | 1| 95| |METAB8 |PATIENT1 | 1| 95| |METAB9 |PATIENT1 | 1| 95| |METAB10 |PATIENT1 | 1| 95|

Vignette Info

Note the various macros within the vignette section of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the title field and the \VignetteIndexEntry to match the title of your vignette.

Styles

The html_vignette template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:

output: 
  rmarkdown::html_vignette:
    css: mystyles.css

Figures

The figure sizes have been customised so that you can easily put two images side-by-side.

plot(1:10)
plot(10:1)

You can enable figure captions by fig_caption: yes in YAML:

output:
  rmarkdown::html_vignette:
    fig_caption: yes

Then you can use the chunk option fig.cap = "Your figure caption." in knitr.

More Examples

You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using knitr::kable().

| | mpg| cyl| disp| hp| drat| wt| qsec| vs| am| gear| carb| |:-----------------|----:|---:|-----:|---:|----:|-----:|-----:|--:|--:|----:|----:| |Mazda RX4 | 21.0| 6| 160.0| 110| 3.90| 2.620| 16.46| 0| 1| 4| 4| |Mazda RX4 Wag | 21.0| 6| 160.0| 110| 3.90| 2.875| 17.02| 0| 1| 4| 4| |Datsun 710 | 22.8| 4| 108.0| 93| 3.85| 2.320| 18.61| 1| 1| 4| 1| |Hornet 4 Drive | 21.4| 6| 258.0| 110| 3.08| 3.215| 19.44| 1| 0| 3| 1| |Hornet Sportabout | 18.7| 8| 360.0| 175| 3.15| 3.440| 17.02| 0| 0| 3| 2| |Valiant | 18.1| 6| 225.0| 105| 2.76| 3.460| 20.22| 1| 0| 3| 1| |Duster 360 | 14.3| 8| 360.0| 245| 3.21| 3.570| 15.84| 0| 0| 3| 4| |Merc 240D | 24.4| 4| 146.7| 62| 3.69| 3.190| 20.00| 1| 0| 4| 2| |Merc 230 | 22.8| 4| 140.8| 95| 3.92| 3.150| 22.90| 1| 0| 4| 2| |Merc 280 | 19.2| 6| 167.6| 123| 3.92| 3.440| 18.30| 1| 0| 4| 4|

Also a quote using >:

"He who gives up [code] safety for [code] speed deserves neither." (via)

miepstei/MetabolonR documentation built on May 22, 2019, 10:50 p.m.