https://github.com/jorainer/unsorted
Unsorted R functions and utilities.
https://github.com/jorainer/unsorted
Last synced: 10 months ago
JSON representation
Unsorted R functions and utilities.
- Host: GitHub
- URL: https://github.com/jorainer/unsorted
- Owner: jorainer
- Created: 2014-09-01T08:07:02.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2016-01-14T15:17:53.000Z (almost 10 years ago)
- Last Synced: 2025-01-20T22:55:04.370Z (11 months ago)
- Language: R
- Size: 35.2 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.org
Awesome Lists containing this project
README
#+TITLE:unsoRted R package
#+AUTHOR: Johannes Rainer
#+email: johannes.rainer@i-med.ac.at
#+OPTIONS: ^:{}
#+INFOJS_OPT:
#+PROPERTY: exports code
#+PROPERTY: session *R*
#+PROPERTY: noweb yes
#+PROPERTY: results output
#+PROPERTY: tangle yes
#+STARTUP: overview
#+INFOJS_OPT: view:t toc:t ltoc:t mouse:underline buttons:0 path:http://thomasf.github.io/solarized-css/org-info.min.js
#+HTML_HEAD:
#+LATEX_HEADER: \usepackage[backend=bibtex,style=chem-rsc,hyperref=true]{biblatex}
#+LATEX_HEADER: \usepackage{parskip}
#+LATEX_HEADER: \setlength{\textwidth}{17.0cm}
#+LATEX_HEADER: \setlength{\hoffset}{-2.5cm}
#+LATEX_HEADER: \setlength{\textheight}{22cm}
#+LATEX_HEADER: \setlength{\voffset}{-1.5cm}
#+LATEX_HEADER: \addbibresource{~/Documents/Unison/Papers2/bib/references.bib}
#+LATEX_HEADER: \usepackage{verbatim}
#+LATEX_HEADER: \usepackage{inconsolata}
#+LATEX_HEADER: \makeatletter
#+LATEX_HEADER: \def\verbatim@font{\scriptsize\ttfamily}
#+LATEX_HEADER: \makeatother
-----
# #+BEGIN_HTML
# [](https://travis-ci.org/jotsetung/unsoRted)
# #+END_HTML
[[https://travis-ci.org/jotsetung/unsoRted][https://travis-ci.org/jotsetung/unsoRted.svg?branch=master]]
* Description
This R package contains some unsorted utilities and functions that might make life easier in the day-to-day use of R for data analysis.
** Functions related to data analysis
+ =getAnnotation=: retrieves an annotation data.frame for a given (Affymetrix based) =ExpressionSet=. For more informations see the according help.
+ =getAnnotationForIDs=: retrieves a data.frame with annotations for the provided feature (probe set) ids. For more informations see the according help.
+ =getRepPS=: returns a representative probe set for a gene based on some criteria. For more informations see the according help.
+ =hyperGGeneric=: performs a category analysis on any user provided definition of categories. For more informations see the according help.
** Visualizations
+ =plotCategoryBar= and =plotCategoryBars=: visualization of category enrichment analysis results.
+ =modColor=, =shiftColor= and =invertColor=: invert or shift colors in RGB or HSV color space.
** Other utilities
+ =convertTxt2Xls=: converts a text file with tabular content to a Microsoft Excel spreadsheet. For more informations see the according help.
+ =load.from.http=: loads a RData file from a remote server (e.g. http or ftp server). For more informations see the according help.
+ =pastedmatch=: value matching allowing e.g. =;= separated values. For more informations see the according help.
+ =read.table.from.http=: loads and reads a table from a remote (e.g. http or ftp) server. For more informations see the according help.
* Development
Please add new functions or improve existing ones. New functions should be documented (=Rd= format) and listed in this document (=README.org=) as well as in =man/unsoRted-package.Rd=. This file should then be exported as a markdown (=md=) file (best performed in Emacs org-mode =c-c c-e=).
** Authors
+ Daniel Bindreither
+ Johannes Rainer
(please add your name to this (=README.org=) file if you edit the code or add new functionality).
** TODOs
*** TODO File =annotation.R=, function =getAnnotation=: speed up the call.
:PROPERTIES:
:ID: 6466E194-27C0-4ACD-AF24-FF5587697DBA
:END:
*** TODO File =annotation.R=: implement annotations for our custom CDFs: automatically download them.
:PROPERTIES:
:ID: 0E3493C1-34D6-4A33-A322-661E781E72C5
:END: