| <!DOCTYPE html> | |
| <html> | |
| <head> | |
| <meta charset="utf-8"> | |
| <meta name="viewport" content="width=device-width"> | |
| <title>Elementary observables</title> | |
| </head> | |
| <body> | |
| <script src="https://unpkg.com/@reactivex/rxjs@5.0.3/dist/global/Rx.js"></script> | |
| <button id='error'>Will throw</button> |
| # bootstrap.R | |
| cat("Loading packages\n") | |
| library(tidyverse) | |
| library(RefFreeEWAS) | |
| library(qvalue) | |
| cat("Loading data\n") | |
| load("pdat.merge.rdata") | |
| load("betas.rdata") |
| [ | |
| // Align | |
| { "keys": ["super+.", "super+a"], "command": "alignment" }, | |
| // Surround | |
| { "keys": ["super+.", "super+s", "super+s"], "command": "surround_selection"}, | |
| { "keys": ["super+.", "super+s", "super+d"], "command": "surround_delete"}, | |
| { "keys": ["super+.", "super+s", "super+c"], "command": "surround_change"}, | |
| // Expand selection | |
| { "keys": ["super+shift+'"], "command": "expand_selection_to_quotes"}, | |
| { "keys": ["super+shift+;"], "command": "expand_selection", "args": {"to": "scope"}}, |
| ```{r, echo=FALSE} | |
| library(magrittr) | |
| ``` | |
| # `%grep%` operator | |
| Using `R`'s built-in `grep` function is really inconvenient for interactive work. | |
| There already exists a convenient `%in%` operator for testing membership in a sequence. | |
| However, real data analysis rarely presents with well-defined sequences. | |
| Strings are much more common. |
For a given KEGG pathway, we want to get a list of all the genes. Ensembl IDs are convenient here.
KEGG provides a REST API for some tasks, but is far from complete. For example, it is possible to map from KEGG to NCBI IDs, but not to Ensembl IDs.
The implementation peforms the following steps:
| #include <vector> | |
| #include <numeric> | |
| #include <random> | |
| using namespace std; | |
| template <typename T> | |
| T sum(vector<T> v) { | |
| return accumulate(v.begin(), v.end(), 0.0); | |
| } |
| template <typename T> | |
| ostream &operator<<(ostream &os, const vector<T> &v) { | |
| os << "["; | |
| typename vector<T>::const_iterator it; | |
| for (it = v.begin(); it != v.end() - 1; ++it) { | |
| os << *it << ", "; | |
| } | |
| os << *(it) << "]"; | |
| return os; | |
| } |
| # Use dots (.) instead of ($) | |
| R_ify <- function(expr) eval(parse(text= | |
| gsub("\\.","$",substitute(expr)))) | |
| R_ify(mtcars.mpg) |
| #Get repo list, filter git urls | |
| GITHUB_NAME=octocat | |
| curl https://api.github.com/users/$GITHUB_NAME/repos > github_response | |
| for repo in `cat github_response | jq -r '.[] | .git_url'`; do; | |
| git clone $repo; | |
| done |
| #this is a simple way to plot a matrix from a txt file | |
| mat_data_frame=read.table("data.txt",header=F) | |
| #rev is there to start plotting M(0,0) in the upper left corner | |
| #col=rainbow(10) uses the rainbow color palette. You can find other ones here: | |
| #http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/palettes.html | |
| image(as.matrix(rev(mat_data_frame)),col=rainbow(10)) |
