#R

In this post, I document the full formula assignment pipeline using MFAssignR, tailored for Orbitrap-MS data post-peak list processing (There is no need to reinvent the wheel here).

The steps include quality control filtering, noise estimation via Kendrick Mass Defect (KMD) plots, isotopic filtering, recalibrant inspection, and final formula assignment.

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Jupyter(即原来的Ipython Notebook Project)基于Web端的实时交互,拥有着极佳的用户体验。同时,Jupyter体系可直接使用其他语言,用户呢能够在同一界面下调用R内核或Python内核(共支持49种),功能十分强大。
在Mac OS下尝试在Jupyter中添加R语言内核,遇到了一些问题,在此记录个人安装过程和诸问题的解决方法。

STEP1 基本软件准备

  • Python和IPython.作为初学者,我直接安装了Python的科学计算发行版Anaconda,其包含了Python2.7并内置很多有用的Package(numpy, SciPy, Matplotlib),Jupyter(Ipython Notebook)以及Spyder(个人感觉类似于R studio的集成开发环境)
  • R 3.2.1(World-Famous Astronaut),官网下载安装即可。

STEP2 有关库的安装

主要工作是为R语言添加IRkernal这一新的Package, 以实现Jupyter对R语言的支持。主要的步骤如下(依照IRkernal的README文档):

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