<!-- README.md is generated from README.Rmd. Please edit that file -->
# idpr
Overall, ‘idpr’ aims to integrate tools for the computational analysis
of intrinsically disordered proteins within R. This package is used to
identify known characteristics of IDPs within a sequence of interest
with easily reported and dynamic results. Additionally, this package
also includes tools for IDP-based sequence analysis to be used in
conjunction with other R packages.
**Please Refer to idpr-vignette.Rmd file for a detailed introduction to
the** **idpr package.**
Links to the vignettes found at the [Bioconductor landing page
(here)](https://doi.org/doi:10.18129/B9.bioc.idpr)
## Installation
You can install the stable release version version from
[Bioconductor](https://doi.org/doi:10.18129/B9.bioc.idpr) with:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("idpr")
```
You can install the development version from
[Bioconductor](https://bioconductor.org/packages/devel/bioc/html/idpr.html)
with:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
```
Or you can install the most recent development version from
[GitHub](https://github.com/wmm27/idpr) with:
``` r
# install.packages("devtools") #if not already installed
devtools::install_github("wmm27/idpr")
```
## Example
This is a basic example to quickly profile your protein of interest:
``` r
library(idpr)
P53_HUMAN <- TP53Sequences[2] #Getting a pre-loaded sequence from idpr
print(P53_HUMAN)
#> P04637|P53_HUMAN
#> "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD"
P53_ID <- "P04637" #Human TP53 UniProt ID
idprofile(sequence = P53_HUMAN, #Generates the Profile
uniprotAccession = P53_ID)
#> [[1]]
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<img src="man/figures/README-example-5.png" width="75%" />
**Please Refer to idpr-vignette.Rmd file for a detailed introduction to
the** **idpr package.** [Link to the Vignette
(here)](https://bioconductor.org/packages/release/bioc/vignettes/idpr/inst/doc/idpr-vignette.html)
## Appendix
### Package citation
``` r
citation("idpr")
#>
#> To cite package 'idpr' in publications use:
#>
#> William M. McFadden and Judith L. Yanowitz (2020). idpr: Profiling
#> and Analyzing Intrinsically Disordered Proteins in R. R package
#> version 1.0.005.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R},
#> author = {William M. McFadden and Judith L. Yanowitz},
#> year = {2020},
#> note = {R package version 1.0.005},
#> }
```
### Additional Information
``` r
Sys.time()
#> [1] "2020-12-23 14:07:28 EST"
Sys.Date()
#> [1] "2020-12-23"
R.version
#> _
#> platform x86_64-apple-darwin17.0
#> arch x86_64
#> os darwin17.0
#> system x86_64, darwin17.0
#> status
#> major 4
#> minor 0.3
#> year 2020
#> month 10
#> day 10
#> svn rev 79318
#> language R
#> version.string R version 4.0.3 (2020-10-10)
#> nickname Bunny-Wunnies Freak Out
```
