https://github.com/lgatto/hyperlopit2015-csv
The pRolocdata hyperLOPIT data, as 3 csv files
https://github.com/lgatto/hyperlopit2015-csv
Last synced: about 2 months ago
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The pRolocdata hyperLOPIT data, as 3 csv files
- Host: GitHub
- URL: https://github.com/lgatto/hyperlopit2015-csv
- Owner: lgatto
- Created: 2015-12-31T10:03:23.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2016-12-15T11:00:09.000Z (over 8 years ago)
- Last Synced: 2025-01-20T23:12:52.431Z (3 months ago)
- Language: Makefile
- Size: 541 KB
- Stars: 0
- Watchers: 3
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
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README
## The `pRolocdata` `hyperLOPIT` data, as csv files
This data originates from the Bioconductor
[`pRolocdata`](http://bioconductor.org/packages/release/data/experiment/html/pRolocdata.html)
package. It is a recent spatial proteomics dataset, formatted and
analysed using the
[`pRoloc`](http://bioconductor.org/packages/release/bioc/html/pRoloc.html)
software.
#### Installation
To install these software:
```r
source("https://bioconductor.org/biocLite.R")
biocLite("pRoloc")
biocLite("pRolocdata")
```
#### Accessing the data
```{r demo, warning=FALSE}
suppressPackageStartupMessages(library("pRolocdata"))
data(hyperLOPIT2015)
class(hyperLOPIT2015)
hyperLOPIT2015
```
This `MSnSet` class is specific to quantitative proteomics data, but
that can be summerised by 2 or 3 tabular data structures (from an R
point of view, 1 [expression `matrix`](./exprs.csv) and 1 or 2
`data.frames` describing the [features](./fdata.csv) and
[samples](./pdata.csv)), which are accessible individually with
```{r exprs}
exprs(hyperLOPIT2015)[1:6, 1:3] ## a matrix
```
```{r fdata}
fData(hyperLOPIT2015)[1:6, 1:3] ## a data.frame
```
```{r pdata}
pData(hyperLOPIT2015)[1:6, 1:3] ## second data.frame
```
#### Producing the csv files
```{r makecsv}
write.csv(exprs(hyperLOPIT2015), file = "exprs.csv")
write.csv(fData(hyperLOPIT2015), file = "fdata.csv")
write.csv(pData(hyperLOPIT2015), file = "pdata.csv")
```
#### Visualisation
```{r plot2d}
pRoloc::plot2D(hyperLOPIT2015)
```
#### Session information
```{r si}
sessionInfo()
```