DOC PREVIEW
Wright BIO 2110 - Rec10_cumulative distributions

This preview shows page 1-2 out of 7 pages.

Save
View full document
View full document
Premium Document
Do you want full access? Go Premium and unlock all 7 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 7 pages.
Access to all documents
Download any document
Ad free experience
Premium Document
Do you want full access? Go Premium and unlock all 7 pages.
Access to all documents
Download any document
Ad free experience

Unformatted text preview:

BIO$2110$–$Recitation$10$ 2$December$2016$QTLs$–$Kolmogorov-Smirnov$test$$Name$______________________$$Names$of$group$members$______________________$$$___________________________$$_______________________$$In$QTL$analyses,$genotypes$are$determined$for$multiple$genetics$markers$(usually$SNP$or$microsatellite$markers)$across$the$genome.$$For$each$marker,$the$population$is$divided$by$genotype.$$Phenotypic$distributions$of$these$genotypes$then$are$compared.$$QTLs$are$identified$(mapped)$thorugh$the$identification$of$markers$for$which$phenotypic$distributions$of$different$genotypes$differ$significantly.$$Usually,$QTL$data$sets$are$quite$large$and$analyses$are$done$computationally.$$However$for$small$data$sets$(and$for$instructors$who$think$there$is$pedagogical$value$in$it),$distributions$can$be$compared$by$hand.$$$$On$the$last$page$of$this$handout,$data$for$the$fruit$weights$and$genotypes$of$BC$progeny$are$given.$$Your$task$is$to$compare$the$weight$distributions$of$B/B$and$B/S$BC$progeny$for$two$of$these$markers$(your$choice)$using$the$Kolmogorov-Smirnov$(K-S)$test.$$In$the$K-S$test,$distributions$first$are$converted$into$cumulative$distributions$(see$below).$$From$these$cumulative$distributions,$a$D-statistic$(the$largest$separation$of$the$cumulative$distributions)$is$determined.$$From$this$D-statistic$and$the$sample$sized$of$each$distribution,$a$p-value$can$be$determined.$$$$$$$Cumulative$Distributions$that$don’t$differ$significantly.$$$$$$$$$$$Cumulative$distributions$that$do$differ$significantly.$$$ $0.000$0.200$0.400$0.600$0.800$1.000$1$ 3$ 5$ 7$ 9$ 11$ 13$ 15$ 17$ 19$ 21$BB$BS$0.000$0.200$0.400$0.600$0.800$1.000$1$ 3$ 5$ 7$ 9$ 11$ 13$ 15$ 17$ 19$ 21$BB$BS$D-stat$Directions:$•$$For$determine$how$many$are$B/B$homozygotes$and$how$many$are$B/S$heterozygotes.$•$$For$each$genotype,$list$the$number$of$individuals$in$each$weight$class.$•$$Determine$the$cumulative$distribution$of$phenotypes$for$each$genotype.$-$$Determine$for$each$weight$class$what$fraction$of$individuals$weigh$that$much$or$less.$-$ e,g,$for$the$M1$marker,$there$are$eight$B/B$homozygotes.$$Three$of$these$weigh$170$gm$or$less.$$Therefore,$at$170,$the$value$for$the$cumulative$distribution$is$3/8$or$0.375.$$It$remains$at$0.375$at$171$and$172$gm$(no$additional$B/B$homozygotes$at$these$weights.$$Four$homozygotes$weigh$173$gm$or$less.$$$So$at$174$gm,$the$cumulative$distribution$value$is$4/8$or$0.500.$$By$185$gm,$the$maximum$weight$recorded,$all$cumulative$distribution$values$for$all$genotypes$at$all$markers$should$be$equal$to1.000.$•$$$For$each$weight$(165$–$185),$determine$the$difference$between$the$cumulative$distributions$for$B/B$homozygotes$and$B/S$heterozygotes.$$$-$this$is$equal$to$the$absolute$value$of$B/B$minus$B/S$$-$e.g.,$for$marker$M1$at$171$gm,$this$is$equal$to$|0.375$–$0.417|$=$0.0412$•$$Identified$the$maximum$difference$between$the$B/B$and$B/S$cumulative$distributions.$-$$This%value,%diffmax,%is%the%D-statistic$•$$go$to$https://home.ubalt.edu/ntsbarsh/Business-stat/otherapplets/pvalues.htm#rkstwo$$ -$$enter$$the$D-statistic,$$the$B/B$sample$size,$the$B/S$sample$size$and$hit$the$compute$button$to$determine$a$P-value$P-values$are$calculated$to$three$decimal$places.$$$Values$less$than$that$are$returned$a s$0.000$•$$On$the$same$graph,$plot$the$cumulative$distributions$for$the$B/B$and$B/S$genotypes.$•$$Indicate$on$this$graph$the$position$from$which$the$D-statistic$was$determined.$$Do%this%for%two%of%the%five%markers.% %$Marker$______$$cumulative$dist.$$BCs$B/B$B/S$$B/B$B/S$|diff|$165$$$$$$$168$$$$$$$169$$$$$$$169$$$$$$$170$$$$$$$170$$$$$$$170$$$$$$$171$$$$$$$173$$$$$$$174$$$$$$$176$$$$$$$179$$$$$$$180$$$$$$$181$$$$$$$182$$$$$$$182$$$$$$$182$$$$$$$183$$$$$$$185$$$$$$$185$$$$$$$N$=$$$$$$$$$$$$$$$$$$D-$sta tistic$=$$$$$$$$$$$$P-value$=$$$$$ $$$Marker$$________$$$$ $1651.0&&&0.9&&&0.8&&&0.7&&&0.6&&&0.5&&&0.4&&&0.3&&&0.2&&&0.1&&&0.0&&167169171173175177179181183185$$$Marker$______$$cumulative$dist.$$BCs$B/B$B/S$$B/B$B/S$|diff|$165$$$$$$$168$$$$$$$169$$$$$$$169$$$$$$$170$$$$$$$170$$$$$$$170$$$$$$$171$$$$$$$173$$$$$$$174$$$$$$$176$$$$$$$179$$$$$$$180$$$$$$$181$$$$$$$182$$$$$$$182$$$$$$$182$$$$$$$183$$$$$$$185$$$$$$$185$$$$$$$N$=$$$$$$$$$$$$$$$$$$D-$sta tistic$=$$$$$$$$$$$$P-value$=$$$$ $$Marker$$________$$$$


View Full Document

Wright BIO 2110 - Rec10_cumulative distributions

Download Rec10_cumulative distributions
Our administrator received your request to download this document. We will send you the file to your email shortly.
Loading Unlocking...
Login

Join to view Rec10_cumulative distributions and access 3M+ class-specific study document.

or
We will never post anything without your permission.
Don't have an account?
Sign Up

Join to view Rec10_cumulative distributions 2 2 and access 3M+ class-specific study document.

or

By creating an account you agree to our Privacy Policy and Terms Of Use

Already a member?