getPXDfile: Download data from PRIDE
In MBQN: Mean/Median-balanced quantile normalization
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
Auxiliary function which downloads selected data, like protein
group intensities, from PRIDE [1].
Usage
1
getPXDfile(pxd_id, source.path = NULL, file.pattern = "proteingroups")
Arguments
pxd_id
the PRIDE identifier.
source.path
pathname where to store and search for the
data file, e.g. "proteinGroups.txt"-file; default = NULL uses current working
directory.
file.pattern
character specifying the kind of dataset for download,
e.g. "proteinGroups" or "peptides".
Details
This function requires the R packages rpx [2] and BiocFileChace.
As a temporary
fix old versions of the rpx package's pxurl and pxfiles function were
included
Value
status (0=ok, 1=not MaxQuant data set, 2=no proteinGroup file)
Author(s)
Ariane Schad
References
[1] Vizca<c3><ad>no JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I,
Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.
2016 update of the PRIDE database and related tools. Nucleic Acids Res.
2016 Jan 1;44(D1): D447-D456. PubMed PMID:26527722.
[2] See "rpx" by Laurent Gatto (2017). rpx: R Interface to the
ProteomeXchange Repository. Package version 1.10.2,
https://github.com/lgatto/rpx.
Examples
1
2
## Download protein LFQ intensities of PXD001584 from PRIDE
getPXDfile(pxd_id = "PXD001584")
MBQN documentation built on Nov. 8, 2020, 8:13 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) References Examples
Description
Auxiliary function which downloads selected data, like protein group intensities, from PRIDE [1].
Usage
1 | getPXDfile(pxd_id, source.path = NULL, file.pattern = "proteingroups")
|
Arguments
pxd_id |
the PRIDE identifier. |
source.path |
pathname where to store and search for the data file, e.g. "proteinGroups.txt"-file; default = NULL uses current working directory. |
file.pattern |
character specifying the kind of dataset for download, e.g. "proteinGroups" or "peptides". |
Details
This function requires the R packages rpx [2] and BiocFileChace. As a temporary fix old versions of the rpx package's pxurl and pxfiles function were included
Value
status (0=ok, 1=not MaxQuant data set, 2=no proteinGroup file)
Author(s)
Ariane Schad
References
[1] Vizca<c3><ad>no JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I,
Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.
2016 update of the PRIDE database and related tools. Nucleic Acids Res.
2016 Jan 1;44(D1): D447-D456. PubMed PMID:26527722.
[2] See "rpx" by Laurent Gatto (2017). rpx: R Interface to the
ProteomeXchange Repository. Package version 1.10.2,
https://github.com/lgatto/rpx.
Examples
1 2 | ## Download protein LFQ intensities of PXD001584 from PRIDE
getPXDfile(pxd_id = "PXD001584")
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.