Rを用いた解析の実例 Project *ぶろったん*
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This document discusses analyzing biomedical literature using R and summarizes statistics on terms from PubMed. It shows how to import a CSV file of PubMed records into R, filter the data by year, and calculate sums of term frequencies. Over 19 million records are in PubMed with over 111,000 containing terms like Southern blotting, Northern blotting, and Western blotting. R can be used to efficiently analyze large text corpora from sources like PubMed.
![Apply
> apply(a[(a$year == 2009),3:10],2,sum)
n N s S e E w W
78 285 10 280 1 1 1950 7077
ID year n N s S e E w W
95117 19145733 2008 0 0 0 0 0 0 1 0
95118 19145310 2008 0 0 0 0 0 0 0 1
95119 19036171 2008 0 0 0 0 0 0 0 1
95120 18585910 2009 0 0 0 1 0 0 0 0
95121 18595762 2009 0 0 0 0 0 0 0 1
95262 18679024 2009 0 1 0 0 0 0 0 0
95263 18573527 2009 0 0 0 0 0 0 0 1
95264 18727094 2009 0 0 0 0 0 0 0 1
95265 18824023 2009 0 0 0 1 0 0 0 0](https://image.slidesharecdn.com/blottan-100509082835-phpapp01/85/R-Project-26-320.jpg)
![Apply
> apply(a[(a$year == 2009),3:10],2,sum)
n N s S e E w W
78 285 10 280 1 1 1950 7077
ID year n N s S e E w W
95117 19145733 2008 0 0 0 0 0 0 1 0
95118 19145310 2008 0 0 0 0 0 0 0 1
95119 19036171 2008 0 0 0 0 0 0 0 1
95120 18585910 2009 0 0 0 1 0 0 0 0
95121 18595762 2009 0 0 0 0 0 0 0 1
95262 18679024 2009 0 1 0 0 0 0 0 0
95263 18573527 2009 0 0 0 0 0 0 0 1
95264 18727094 2009 0 0 0 0 0 0 0 1
95265 18824023 2009 0 0 0 1 0 0 0 0](https://image.slidesharecdn.com/blottan-100509082835-phpapp01/85/R-Project-27-320.jpg)
![Apply
> apply(a[(a$year == 2009),3:10],2,sum)
n N s S e E w W
78 285 10 280 1 1 1950 7077
ID year n N s S e E w W
95117 19145733 2008 0 0 0 0 0 0 1 0
95118 19145310 2008 0 0 0 0 0 0 0 1
95119 19036171 2008 0 0 0 0 0 0 0 1
95120 18585910 2009 0 0 0 1 0 0 0 0
95121 18595762 2009 0 0 0 0 0 0 0 1
95262 18679024 2009 0 1 0 0 0 0 0 0
95263 18573527 2009 0 0 0 0 0 0 0 1
95264 18727094 2009 0 0 0 0 0 0 0 1
95265 18824023 2009 0 0 0 1 0 0 0 0](https://image.slidesharecdn.com/blottan-100509082835-phpapp01/85/R-Project-28-320.jpg)
![Apply
> apply(a[(a$year == 2009),3:10],2,sum)
n N s S e E w W
78 285 10 280 1 1 1950 7077
ID year n N s S e E w W
95117 19145733 2008 0 0 0 0 0 0 1 0
95118 19145310 2008 0 0 0 0 0 0 0 1
95119 19036171 2008 0 0 0 0 0 0 0 1
95120 18585910 2009 0 0 0 1 0 0 0 0
95121 18595762 2009 0 0 0 0 0 0 0 1
95262 18679024 2009 0 ...
1 0 0 0 0 0 0
95263 18573527 2009 0 0 0 0 0 0 0 1
95264 18727094 2009 0 0 0 0 0 0 0 1
95265 18824023 2009 0 0 0 1 0 0 0 0](https://image.slidesharecdn.com/blottan-100509082835-phpapp01/85/R-Project-29-320.jpg)
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Rを用いた解析の実例 Project *ぶろったん*
- 1. R Project * * Tsukuba.R #7 yag_ays
- 2. yag_ays • • • • • Bioinfomatics http://twitter.com/yag_ays
- 3. Research Assistant • DBCLS • TV • R • R ect... • DNA
- 5. Southern blotting 1975 Edwin M. Southern "Detection of specific sequences among DNA fragments separated by gel electrophoresis" 1978 ”Southern blotting”
- 6. Northern, and Western • Southern blotting Northern blotting Western blotting (Eastern )
- 7. Experiments Central dogma Southern blotting DNA Northern blotting RNA Western blotting Protein
- 8. • Southern blotting Southern • “Southern” • Northern blotting Western blotting •
- 11. • • • • •
- 12. 1 •
- 13. 2. inMeXes • http://docman.dbcls.jp/im/index.html
- 16. • •
- 17. • *thern blotting ..etc
- 19. PubMed *thern blotting *thern blotting
- 20. R
- 21. Ruby
- 22. Ruby R • XML •R ... • Ruby xml parser nokogiri
- 23. • Ruby • R • R
- 24. csv > a <- read.csv("medline.csv",header=T) > head(a) ID year n N s S e E w W 1 721776 1978 0 0 0 1 0 0 0 0 2 364479 1978 0 0 0 1 0 0 0 0 3 220264 1979 0 0 0 1 0 0 0 0 4 377232 1979 0 0 0 1 0 0 0 0 5 221902 1979 0 0 0 1 0 0 0 0 6 455450 1979 0 0 0 1 0 0 0 0
- 25. > table(a$year) 1978 1979 1980 1981 1982 1983 1984 1985 1986 2 18 38 77 122 231 392 621 913 1987 1988 1989 1990 1991 1992 1993 1994 1995 1233 1692 2135 2515 2899 3368 3744 3973 4131 1996 1997 1998 1999 2000 2001 2002 2003 2004 4316 4579 4697 4868 4844 5047 4957 5352 5673 2005 2006 2007 2008 2009 2010 6039 6236 6413 7167 9583 3939
- 26. Apply > apply(a[(a$year == 2009),3:10],2,sum) n N s S e E w W 78 285 10 280 1 1 1950 7077 ID year n N s S e E w W 95117 19145733 2008 0 0 0 0 0 0 1 0 95118 19145310 2008 0 0 0 0 0 0 0 1 95119 19036171 2008 0 0 0 0 0 0 0 1 95120 18585910 2009 0 0 0 1 0 0 0 0 95121 18595762 2009 0 0 0 0 0 0 0 1 95262 18679024 2009 0 1 0 0 0 0 0 0 95263 18573527 2009 0 0 0 0 0 0 0 1 95264 18727094 2009 0 0 0 0 0 0 0 1 95265 18824023 2009 0 0 0 1 0 0 0 0
- 27. Apply > apply(a[(a$year == 2009),3:10],2,sum) n N s S e E w W 78 285 10 280 1 1 1950 7077 ID year n N s S e E w W 95117 19145733 2008 0 0 0 0 0 0 1 0 95118 19145310 2008 0 0 0 0 0 0 0 1 95119 19036171 2008 0 0 0 0 0 0 0 1 95120 18585910 2009 0 0 0 1 0 0 0 0 95121 18595762 2009 0 0 0 0 0 0 0 1 95262 18679024 2009 0 1 0 0 0 0 0 0 95263 18573527 2009 0 0 0 0 0 0 0 1 95264 18727094 2009 0 0 0 0 0 0 0 1 95265 18824023 2009 0 0 0 1 0 0 0 0
- 28. Apply > apply(a[(a$year == 2009),3:10],2,sum) n N s S e E w W 78 285 10 280 1 1 1950 7077 ID year n N s S e E w W 95117 19145733 2008 0 0 0 0 0 0 1 0 95118 19145310 2008 0 0 0 0 0 0 0 1 95119 19036171 2008 0 0 0 0 0 0 0 1 95120 18585910 2009 0 0 0 1 0 0 0 0 95121 18595762 2009 0 0 0 0 0 0 0 1 95262 18679024 2009 0 1 0 0 0 0 0 0 95263 18573527 2009 0 0 0 0 0 0 0 1 95264 18727094 2009 0 0 0 0 0 0 0 1 95265 18824023 2009 0 0 0 1 0 0 0 0
- 29. Apply > apply(a[(a$year == 2009),3:10],2,sum) n N s S e E w W 78 285 10 280 1 1 1950 7077 ID year n N s S e E w W 95117 19145733 2008 0 0 0 0 0 0 1 0 95118 19145310 2008 0 0 0 0 0 0 0 1 95119 19036171 2008 0 0 0 0 0 0 0 1 95120 18585910 2009 0 0 0 1 0 0 0 0 95121 18595762 2009 0 0 0 0 0 0 0 1 95262 18679024 2009 0 ... 1 0 0 0 0 0 0 95263 18573527 2009 0 0 0 0 0 0 0 1 95264 18727094 2009 0 0 0 0 0 0 0 1 95265 18824023 2009 0 0 0 1 0 0 0 0
- 30. • PubMed 19,000,000 • 111,579 • Southern blotting 21,243 • Northern blotting 14,608 • Western blotting 79,137
- 33. Southern • •
- 35. • Southern blotting • Northern blotting Western blotting •
- 36. Wikipedia northern- western- • •
- 37. R • • • &R
- 38. • • Wikipedia ...
- 39. Thanks • @bonohu, @chalkless, • @iNut, @mickey24, @syou6162, @y_benjo, @wakuteka • 2 - - http://www.toyobo.co.jp/seihin/xr/lifescience/ products/product/jisshirei/archives/ 2007/02/20072g.html