thomaskelder

## Get pathway edit history from wikipathways.org and export as gource log file
## Run using:
## python wikipathways2gource.py wikipathways.log
## View in gourse using:
## gource -1280x720 -a 3 --seconds-per-day 0.01 --hide dirnames,filenames --user-filter MaintBot --key wikipathways.log
## Create video with gource using:
## gource -1280x720 -a 2 --seconds-per-day 0.005 --hide dirnames,filenames --user-filter MaintBot --key --stop-at-end -o - wikipathways.log | ffmpeg -y -r 30 -f image2pipe -vcodec ppm -i - -vcodec libvpx -b 10000K wikipathways.webm

## Known issues/shortcomings:
## - Pathway ontology terms can have multiple parents, this is ignored, only first is taken here to prevent pathways from showing multiple times in the visualization

thomaskelder

## Fill out your own dbNP user / pass here
authenticate("****", "****", "****")

studies = getStudies()

studyName = "NutriTechHIS"

study = studies[[grep(studyName, sapply(studies, function(x) x$code))]]
studyToken = study['token']

thomaskelder

## Test script to get NutriTech data from dbNP
## Crashes with:
## > source('~/projects/nutritech/code/dbnp.test.R')
## Clinical Chemistry
## Questionnaire Physical Activity
## Error in x$name : $ operator is invalid for atomic vectors

require(GSCFClient)
require(GSCFRUtils)

thomaskelder

library(limma)
library(lumiMouseAll.db)

nu.ids = rownames(data) ## A list of lumi nuIDS
nu.annot = nuID2IlluminaID(nu.ids, lib.mapping = "lumiMouseIDMapping", idType = "All")

## Get entrez ids and gene names

geneNames = as.character(as.list(lumiMouseAllGENENAME)[nu.ids])
entrezIds = as.character(as.list(lumiMouseAllENTREZID)[nu.ids])

thomaskelder

#############################
#### Apply functions     ####
#############################
matrixData = matrix(1:40, nrow = 10, ncol = 4)

### Median of rows
## Using for loop
rowm = rep(NA, nrow(matrixData))
for(r in 1:nrow(matrixData)) {
  rowm[r] = median(matrixData[r,])

thomaskelder

## Only first time: install bioconductor package for your affy array
## Find the proper package here: http://www.bioconductor.org/packages/release/data/annotation/
source("http://bioconductor.org/biocLite.R")
biocLite("hgu95d.db")

## Load the affy annotation library
library(hgu95d.db)

ids = read.delim("omzetten ids.txt", as.is=T, header=T)