getdata-video.R

library("RMySQL")
ucscDb<-dbConnect(MySQL(),user="genome",host="genome-mysql.cse.ucsc.edu")
result<-dbGetQuery(ucscDb,"show databases;");dbDisconnect(ucscDb);

hg19<-dbConnect(MySQL(),user="genome",host="genome-mysql.cse.ucsc.edu",db="hg19")
allTables<-dbListTables(hg19);
length(allTables);

dbListFields(hg19,"affyU133Plus2");

dbGetQuery(hg19, "select count(*) from affyU133Plus2")
affyData<-dbReadTable(hg19,"affyU133Plus2")

head(affyData)

query<-dbSendQuery(hg19,"select * from affyU133Plus2 where misMatches between 1 and 3")
affyMis<-fetch(query); quantile(affyMis$misMatches)

affyMisSmall<-fetch(query,n=10); dbClearResult(query);

dim(affyMisSmall)

dbDisconnect(hg19);


library(rhdf5)
created=h5createFile("example.h5")
created

# create groups
created=h5createGroup("example.h5","foo")
created=h5createGroup("example.h5","baa")
created=h5createGroup("example.h5","foo/foobaa")
h5ls("example.h5")

# write to groups
A=matrix(1:10, nr=5, nc=2)
h5write(A,"example.h5","foo/A")
B=array(seq(0.1,2.0,by=0.1),dim=c(5,2,2))
attr(B,"scale")<-"liter"
h5write(B,"example.h5","foo/foobaa/B")
h5ls("example.h5")

# write dataset
df=data.frame(1L:5L,seq(0,1,length.out=5),c("ab","cde","fgi","a,","s"),stringsAsFactors=FALSE)
h5write(df,"example.h5","df")
h5ls("example.h5")

# reading data
readA=h5read("example.h5","foo/A")
readB=h5read("example.h5","foo/foobaa/B")
readdf=h5read("example.h5","df")
readA
readB
readdf

# writing and reading chunks
h5write(c(12,13,14),"example.h5","foo/A",index=list(1:3,1))
h5read("example.h5","foo/A")

con=url("http://scholar.google.com/citations?user=HI-I6C0AAAAJ&hl=en")
htmlCode=readLines(con)

library(XML)
url="http://scholar.google.com/citations?user=HI-I6C0AAAAJ&hl=en"
html<-htmlTreeParse(url,useInternalNodes=T)
xpathSApply(html, "//title", xmlValue)
xpathSApply(html,"//td[@id='col-citedby']",xmlValue)

# GET using httr
library(httr)
html2=GET(url)
content2=content(html2,as="text")
parsedHtml=htmlParse(content2,asText=TRUE)
xpathSApply(parsedHtml,"//title",xmlValue)

pg1=GET("http://httpbin.org/basic-auth/user/passwd")
pg1

pg2=GET("http://httpbin.org/basic-auth/user/passwd",authenticate("user","passwd"))
pg2
names(pg2)

# handles
google=handle("http://google.com")
pg1=GET(handle=google,path="/")
pg2=GET(handle=google,path="search")


# getting data from APIs
library(httr)
library(rjson)
myapp=oauth_app("twitter",key="GWE6EG0aZxrZHYmO3ztg",secret="OmvwtODFrHGRorfMurjn0mWZTJopsz2hNJZLaZDXFYs")
sig=sign_oauth1.0(myapp,token="463708342-lihrJNiHNi5OjCWifyFuJCQDqNlKpjlwHubbrDKe",token_secret="iMXPx2zO6xhymDZ1wplSTZx8Tt4KKqnfzHIZ6Ju3Cs")
homeTL=GET("https://api.twitter.com/1.1/statuses/home_timeline.json",sig)
json1=content(homeTL)
json2=jsonlite::fromJSON(toJSON(json1))
json2[1,1:4]