R
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==Tutorials== | ==Tutorials== | ||
- | *R [http://www.bioconductor.org/ Bioconductor] | + | :*R [http://www.bioconductor.org/ Bioconductor] |
- | + | ::Bioconductor [http://bioconductor.org/help/course-materials/ course materials] | |
- | + | :::[http://bioconductor.org/help/course-materials/2010/SeattleJan10/ 2010 introductory course] | |
- | *R [http://bm2.genes.nig.ac.jp/RGM2/index.php?clear=all Graphical Manual] | + | |
+ | :*R [http://bm2.genes.nig.ac.jp/RGM2/index.php?clear=all Graphical Manual] | ||
+ | |||
+ | :*[http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000482 A Quick Guide to Teaching R Programming to Computational Biology Students] - PLoS CompBio | ||
+ | |||
===Tips=== | ===Tips=== | ||
- | + | :The script editor with R.gui is a convenient tool (c.f. ESS with Emacs) | |
- | + | ::Command + Enter (OS X) or Ctrl + R (windows) | |
==Packages== | ==Packages== | ||
Line 34: | Line 38: | ||
===seqinr=== | ===seqinr=== | ||
===[http://bioconductor.org Bioconductor]=== | ===[http://bioconductor.org Bioconductor]=== | ||
+ | *[http://bioconductor.org/help/course-materials/ course materials] | ||
+ | **[http://bioconductor.org/help/course-materials/2010/SeattleJan10/ 2010 introductory course] | ||
==Examples== | ==Examples== | ||
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cof[1:10,1:10] | cof[1:10,1:10] | ||
</pre> | </pre> | ||
+ | |||
+ | <pre> | ||
+ | |||
+ | select m1.CUI,m1.SAB,m1.STR,m1.SDUI,m2.CUI,m2.SAB,m2.STR,m2.SDUI from MRCONSO as m1, MRCONSO as m2 where ((m1.CUI=m2.CUI AND m1.LUI=m2.LUI) AND (m1.SAB='MSH' AND m2.SAB='OMIM')) AND m1.TTY='MH' limit 5; | ||
+ | |||
+ | |||
+ | mysql> select CUI,LUI,CODE,SAB,ATV from MRSAT where SAB='MSH' AND ATN='MN' AND ATV like 'C%' limit 5; | ||
+ | |||
+ | mysql> select * from MRDOC where EXPL like 'OMIM%' limit 10; | ||
+ | mysql> select count(distinct CODE) from MRSAT where SAB='OMIM'; | ||
+ | mysql> select count(ATV) from MRSAT where SAB='OMIM' AND ATN='GENESYMBOL'; | ||
+ | mysql> select count(distinct ATV) from MRSAT where SAB='OMIM' AND ATN='GENESYMBOL'; | ||
+ | |||
+ | mysql> select * from MRCONSO where CUI='C0000744' AND SAB='MTHICD9' AND TS='P'; | ||
+ | |||
+ | |||
+ | library(DBI) | ||
+ | library(RMySQL) | ||
+ | drv = dbDriver("MySQL") | ||
+ | con = dbConnect(drv,username='igchoi',password='13579',dbname='umls') | ||
+ | que = "select distinct CUI,CODE from MRSAT where SAB=\'OMIM\'" | ||
+ | ret = dbSendQuery(con,statement=que) | ||
+ | # parsing | ||
+ | ret = unlist(fetch(ret,n=-1)) | ||
+ | ret = matrix(ret,length(ret)/2,2) | ||
+ | print(dim(ret)) | ||
+ | tot = cbind(ret,rep(NA,nrow(ret))) | ||
+ | # omim2icd9 | ||
+ | for (i in 1:nrow(qret)) { | ||
+ | print(i) | ||
+ | qi=paste("select CODE from MRCONSO where CUI=\'",ret[i,1],"\' AND SAB=\'MTHICD9\' AND TS=\'P\'",sep="") | ||
+ | v = dbSendQuery(con,statement=qi) | ||
+ | v = unlist(fetch(v,n=1)) | ||
+ | if(length(v)>0) { tot[i,3] = v } | ||
+ | print(i) | ||
+ | } | ||
+ | print(tot[,3]) | ||
+ | save.image(file="omim2icd.rdata") | ||
+ | </pre> | ||
+ | |||
==Links== | ==Links== | ||
*[http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html News article about R] in NYTimes | *[http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html News article about R] in NYTimes |
Latest revision as of 08:56, 28 May 2011
|
Tutorials
-
- Bioconductor course materials
Tips
- The script editor with R.gui is a convenient tool (c.f. ESS with Emacs)
- Command + Enter (OS X) or Ctrl + R (windows)
Packages
- Installed @panflam, @panpyro
ape
- an object of class "phylo" with the following components:
- edge a two-column matrix of mode numeric where each row represents an edge of the tree; the nodes and the tips are symbolized with numbers; the tips are numbered 1, 2, ..., and the nodes are numbered after the tips. For each row, the first column gives the ancestor.
- edge.length (optional) a numeric vector giving the lengths of the branches given by edge.
- tip.label a vector of mode character giving the names of the tips; the order of the names in this vector corresponds to the (positive) number in edge.
- Nnode the number of (internal) nodes.
- node.label (optional) a vector of mode character giving the names of the nodes.
- root.edge (optional) a numeric value giving the length of the branch at the root if it exists.
DBI
seqinr
Bioconductor
Examples
UMLS
library(RMySQL) library(DBI) drv = dbDriver("MySQL") con = dbConnect(drv,username='',password='',dbname='') que = "select CUI1,CUI2,COF from MRCOC where SAB=\'CCPSS\'" ccpss = dbSendQuery(con,statement=que) ccpss.all = unlist(fetch(ccpss,n=-1)) ccpss.all = matrix(ccpss.all,length(ccpss.all)/3,3) colnames(ccpss.all) = c('CUI1','CUI2','COF') tmp = unique(c(ccpss.all[,1],ccpss.all[,2])) cof = matrix(NA,10877,10877) dimnames(cof) = list(tmp,tmp) apply(ccpss.all,1,function(x) { cof[x[1],x[2]]=x[3] }) cof[1:10,1:10]
select m1.CUI,m1.SAB,m1.STR,m1.SDUI,m2.CUI,m2.SAB,m2.STR,m2.SDUI from MRCONSO as m1, MRCONSO as m2 where ((m1.CUI=m2.CUI AND m1.LUI=m2.LUI) AND (m1.SAB='MSH' AND m2.SAB='OMIM')) AND m1.TTY='MH' limit 5; mysql> select CUI,LUI,CODE,SAB,ATV from MRSAT where SAB='MSH' AND ATN='MN' AND ATV like 'C%' limit 5; mysql> select * from MRDOC where EXPL like 'OMIM%' limit 10; mysql> select count(distinct CODE) from MRSAT where SAB='OMIM'; mysql> select count(ATV) from MRSAT where SAB='OMIM' AND ATN='GENESYMBOL'; mysql> select count(distinct ATV) from MRSAT where SAB='OMIM' AND ATN='GENESYMBOL'; mysql> select * from MRCONSO where CUI='C0000744' AND SAB='MTHICD9' AND TS='P'; library(DBI) library(RMySQL) drv = dbDriver("MySQL") con = dbConnect(drv,username='igchoi',password='13579',dbname='umls') que = "select distinct CUI,CODE from MRSAT where SAB=\'OMIM\'" ret = dbSendQuery(con,statement=que) # parsing ret = unlist(fetch(ret,n=-1)) ret = matrix(ret,length(ret)/2,2) print(dim(ret)) tot = cbind(ret,rep(NA,nrow(ret))) # omim2icd9 for (i in 1:nrow(qret)) { print(i) qi=paste("select CODE from MRCONSO where CUI=\'",ret[i,1],"\' AND SAB=\'MTHICD9\' AND TS=\'P\'",sep="") v = dbSendQuery(con,statement=qi) v = unlist(fetch(v,n=1)) if(length(v)>0) { tot[i,3] = v } print(i) } print(tot[,3]) save.image(file="omim2icd.rdata")
Links
- News article about R in NYTimes