DokuWiki
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/
2008-07-02T14:31:48+01:00DokuWiki
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/lib/images/favicon.icotext/html2008-06-27T14:42:24+01:00Tova Fuller (tova@10.47.163.148)todo -
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/todo?do=diff&1214602944
Running To Do List: Get new picture for the SNP 2.0 code and update the document Repeat analysis with case-control status permuted & check LEO scores Look up SKP1A: Literature review Mutagenesis Ubiquitination & ALS, PD Miscellaneous...text/html2008-02-27T10:48:59+01:00Tova Fuller (tova@10.47.163.167)start
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/start?do=diff&1204138139
Visit the index for easy navigation. The categories I have made include: A Short Reading List & References: References to papers, talks and websites of interest, sorted by year Papers pertaining to my work during the summer of 2005 Papers...text/html2008-02-26T14:35:19+01:00Tova Fuller (tova@76.172.86.171)r:install
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/r:install?do=diff&1204065319
Not to reinvent the wheel, there is a good primer for installing packages on a different R wiki. One can install directly from CRAN if one has an internet connection: install.packages("mypkg", dependencies = TRUE) Or, one can install ma...text/html2007-04-09T21:58:56+01:00Tova Fuller (tova@76.172.68.228)dictionary:d-separation - created
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/dictionary:d-separation?do=diff&1176181136
From Bill Shipley’s “Cause and Correlation in Biology: A user’s guide to path analysis, structural equations and causal inference”, pp 29-30. I(X,Q,Y) - X and Y are d-separated when conditioned on the set Q if: First list e...text/html2007-01-15T01:31:44+01:00Tova Fuller (tova@76.174.28.103)literature:thomas_et_al_2004
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/literature:thomas_et_al_2004?do=diff&1168853504
Reference here1) Introduction Davey Smith and Ebrahim 2) showed that “the magnitude of the estimated effects of a gene (G) on an intermediate phenotype (IP) and on disease (D) can be combined to yield an estimate of the causal effect of th...text/html2007-01-12T21:09:26+01:00Tova Fuller (tova@76.174.28.103)references:2007
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/references:2007?do=diff&1168664966
Papers Thomas DC, Conti DV. (2004) Commentary: The concept of 'Mendelian randomization'. International Epidemiological Association 33:21-25. ...text/html2007-01-12T20:38:41+01:00Tova Fuller (tova@76.174.28.103)r:unlist - created
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/r:unlist?do=diff&1168663121
unlist()1) Given a list structure ‘x’, ‘unlist’ simplifies it to produce a vector which contains all the atomic components which occur in ‘x’. Example: output=c(list, unlist(tobeunlisted)) 1) R documentation ...text/html2007-01-12T20:26:25+01:00Tova Fuller (tova@76.174.28.103)r:match - created
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/r:match?do=diff&1168662385
match()1) ‘match’ returns a vector of the positions of (first) matches of its first argument in its second. Example: reorder=match(stuff, morestuff) 1) R documentation ...text/html2007-01-12T20:23:49+01:00Tova Fuller (tova@76.174.28.103)r:gsub - created
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/r:gsub?do=diff&1168662229
gsub()1) ‘sub’ and ‘gsub’ perform replacement of matches determined by regular expression matching. Example: newvector=gsub("firsttext", "replacement",thevector) We replace the “firsttext” ...text/html2007-01-12T19:59:01+01:00Tova Fuller (tova@76.174.28.103)r:grep
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/r:grep?do=diff&1168660741
grep()1) ‘grep’ searches for matches to ‘pattern’ (its first argument) within the character vector ‘x’ (second argument). ‘regexpr’ and ‘gregexpr’ do too, but return more detail in a diffe...text/html2006-12-04T05:08:44+01:00Tova Fuller (tova@24.55.49.100)biologicaldictionary:chronicallograftnephropathy
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/biologicaldictionary:chronicallograftnephropathy?do=diff&1165237724
Joosten SA, Sijpkens YWJ, Van Kooten C, Paul LC. 2005. Chronic renal allograft rejection: Pathophysiologic considerations Kidney International 68:1-13. Notes from Joosten et al.: Histopathology “fibrous intimal thickening of arteries, glome...text/html2006-11-17T08:47:37+01:00Tova Fuller (tova@207.188.236.196)dictionary:principal_components_analysis - created
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/dictionary:principal_components_analysis?do=diff&1163782057
Read this: http://public.lanl.gov/mewall/kluwer2002.html ...text/html2006-11-02T21:42:57+01:00Tova Fuller (tova@24.55.49.100)r:help.search - created
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/r:help.search?do=diff&1162532577
help.search(”string”) allows you to search the help guide for the specified string from within R. ...text/html2006-11-02T01:37:33+01:00Tova Fuller (tova@24.55.49.100)dictionary:association_test - created
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/dictionary:association_test?do=diff&1162460253
The chi-square test is a non-parametric test to determine if two samples are different enough to reject a null hypothesis that both are essentially the same. The association chi-square test is based on comparing - say - allele frequencies between d...text/html2006-10-24T15:40:26+01:00Tova Fuller (tova@164.67.97.157)dictionary:lcms
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/dictionary:lcms?do=diff&1161729626
This wiki article is based on work by Schadt et. al.. We assume there is a QTL, which we will name L, that drives a gene (R) and a clinical trait (L). We can use Markov properties for three simple models that consider each of the causality relation...text/html2006-10-24T14:49:31+01:00Tova Fuller (tova@164.67.97.157)references:2006
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/references:2006?do=diff&1161726571
References, 2006 Papers Chronic Fatigue Syndrome Paper Presson A, Sobel E, Papp J, Lusis AJ, Horvath S. [date] Integration of Genetic and Genomic Approaches for the Analysis of Chronic Fatigue Syndrome Implicates Forkhead Box N1 Mouse Genetics...text/html2006-09-23T12:41:44+01:00Tova Fuller (tova@24.55.49.100)r:merge
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/r:merge?do=diff&1159040504
The command merge is used to merge two data sets by a given column. Where things become tricky is when one data frame has duplicate entries in the row that is being merged on. Below I give an example of how this can be avoided. Example dat0All=rea...text/html2006-09-23T12:38:56+01:00Tova Fuller (tova@24.55.49.100)r:ifelse
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/r:ifelse?do=diff&1159040336
“ifelse returns a value with the same shape as test which is filled with elements selected from either yes or no depending on whether the element of test is TRUE or FALSE.” “Usage: ifelse(test, yes, no) test: an object which can ...text/html2006-09-14T13:54:53+01:00Tova Fuller (tova@164.67.97.151)r:pdf - created
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/r:pdf?do=diff&1158267293
To export the plot you wish to make in pdf format, you use the following commands: pdf(file="thisisthenameofthepdf.pdf") blah blah blah blahblahblah dev.off() ...text/html2006-09-13T21:04:28+01:00Tova Fuller (tova@24.55.49.100)dictionary:kruskal_wallis
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/wiki/dictionary:kruskal_wallis?do=diff&1158206668
The Kruskal Wallis test determines if k population means are equal. ni represents sample sizes for k groups, and Ri is the sum of the ranks for group i. Test statistic The Kruskal Wallis test statistic is with a chi square distribution of k-...