statistical resources - course notes, materilas, Ingo Ruczinski John Hopkins university

GOODNESS OF FIT, lack of fit test, statistics

biostatistical genetics and genetic epidemiology by Elston
-- GOODNESS OF FIT

lack of fit test
XXXXX NIST

with examples in R in pdf

Model selection in ecology Johnson 2004 REVIEW PDF

genetic models CLARIFICATIONS NEEDED

KEYWORDS TO BE CLARIFIED



allelic association, genotypic association (PLINK)



genotype relative risk



allele risk



genetic models = diallelic polymorphisms:

dominant

recessive

co-dominant

overdominant

additive (log-additive)

multiplicative



cf PLINK tutorial section Association

cf Moreno et al. SNPstats

cf Lewis 2002: Genetic association studies: design, analysis interpretation.

cf Handbook of Statistical genetics. Eds. Balding, Bishop ...: chapters 36, 37 by Clayton, and Morris/Cardon

cf SNPGWA tutorial - gives exact documentation for calculations. explains CochranArmitage TREND TEST for log-additive genetic/inheritance model. involves NEWTON-RAPHSON algorithm /iterative process/ simply --- complicated



cf summarize - assumptions of HWE for allelic multiplicative, genotypic tests??

-

can log-additive be computed in SPSS

cf coding recommendations by CLAYTON, Morris -- logistic reg model including ADDITIVE and DOMINANCE factor.

- furthermore - cf likelihood ratio tests for model selection, cf Moreno aIC, BIC...



cf MODELS for binary data /disease status/ and for quantitative phenotypes.

confidence intervals, odds ratio

general intro on confidence intervals by Steve Simon /children mercy



odds ratio and confidence interval calculation XXX

GENETIC EPIDEMIOLOGY BASICS

https://courses.washington.edu/b516/lectures/handout9.pdf



Genotypic and Allelic Association for Binary traits TUTORIAL IN STATA

ODDS RATIO IN association testing - includes worked example, incl. formula for 95CI calculation /Woolf



genetic ANALYSIS OF complex disease GOOGLEBOOK



GENETIC ASSOCIATION STUDIES EXPLAINED - A PRIMER

ELEMENTARY CLASSICAL GENETICS





/ASSOCIATION TESTING Rpackage by clayton

hardy weiberg equilibrium, population genetics

Online Encyclopedia for Genetic Epidemiology
nice resource but seems to lack updates since 2007 ___???
inclued tool for HWE calculation ˇ(but doesn t provide exact p values)

DORAK POPGEN XXXXXXXX ______XXXXXXX
extensive collection of text on genetics, genetic epidemiology, genetic statistics etc (as mentioned repeatedly in this blog)
slight disadvantage - layout is rather poor. lumps of text
- nice addition - music notes


Michael Court excel template for HWE calculation. simple. works fine
www.tufts.edu/~mcourt01/Documents/Court%20lab%20-%20HW%20calculator.xls


evolutionary statistics - evomaths HWE test principle explained


http://de.wikipedia.org/wiki/Hardy-Weinberg-Gleichgewicht DEUTSCH
includes letter by Hardy to Editor of Science: "I am reluctant to intrude in a discussion concerning matters of which I have no expert knowledge, and I should have expected the very simple point which I wish to make to have been familiar to biologists."""

eine schoene erläuterung von Hardy-Weinberg-Gleichgewicht DEUTSCH PPT

Hardy Weinberg EQUILIBRIUM explained .... from Kimballs Biology pages NICE

populační genetika CZECH vedecko populárny resp. pre gymnazia

HWE, theory _ calculation applet + explanation /danish author NICE . population genetics

aktualni genetika Šeda, Šedová Liška, - vybrané kapitoly z lékarskej genetiky, genomiky, biologie.

sim8 applet for allele frequencie, HWE, allele frequencies based on different evolutionary and biological factors -- COMPLICATED

pharmacogenomics database EXTRACTION

http://www.pharmgkb.org/search/pathway/anti-diabetic/anti-diabetic-pd.jsp#tabview=tab0