Package xtal. December 29, 2015
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1 Type Package Title Crystallization Toolset Version 1.15 Date Author Maintainer Qingan Sun Package xtal December 29, 2015 This is the tool set for crystallographer to design and analyze crystallization experiments, especially for ribosome from Mycobacterium tuberculosis. License GPL-2 GPL-3 Depends methods,graphics, grdevices, stats, utils LazyLoad yes NeedsCompilation no Repository CRAN Date/Publication :31:03 R topics documented: xtal-package Design-class design2screen design2screen-methods design8vertex Design8Vertex-class Exp-class getcondition getcondition-methods getoptimal getoptimal-methods screen Screen-class screencsv screencsv-methods
2 2 Design-class writetecan writetecan-methods Index 13 xtal-package Crystallization Tool Details This is the tool set for crystallographer to design and analyze crystallization experiments, especially for ribosome from Mycobacterium tuberculosis. Package: xtal Type: Package Version: 1.0 Date: License: GPL-2 GPL-3 Depends: methods,graphics, grdevices, stats, utils Maintainer: Qingan Sun Design-class Class "Design" Virtual Class of the experiment design Objects from the Class A virtual Class: No objects may be created from it. Slots volume: Object of class "numeric" volume of each well in matrix block stock: Object of class "data.frame" stock composition portion: Object of class "array" portion of each stock in each well
3 design2screen 3 design2screen signature(object = "Design"):... See Also Design8Vertex showclass("design") design2screen Constructor of Screen from Design object extract matrix info from Design object and put into new Screen object design2screen(object) object Design class Value new Screen object # set up a Design object # please read the design8vertex for detail stock=matrix(nrow=8,ncol=3) colnames(stock)=c("peg","ph","salt") stock[,1]=rep(c(6,16),4) stock[,2]=rep(c(8,8,9.5,9.5),2) stock[,3]=rep(c(0,300),each=4) stock=data.frame(stock) dim=list(5:0/5,3:0/3,3:0/3)
4 4 design8vertex test8vertex=design8vertex(900,stock,dim) # construct a new Screen object testscreen<-design2screen(test8vertex) design2screen-methods ~~ for Function design2screen ~~ ~~ for function design2screen ~~ signature(object = "Design") constructor of Screen from Design object design8vertex constructor of Class Design8Vertex Caculate the portion matrix of each stock from the dim, and call the new(design8vertex) design8vertex(volume, stock, dim) volume stock dim numeric, for volume of each well in matrix block dataframe, the composition of each stock (8 stock in the 8-vertex design) list of three vectors, the dilution of stock 1 in 3 dimensions: 6X4X4 Value new object of Design8Vertex class
5 Design8Vertex-class 5 # set the stock with 3 variables: PEG concentration, ph, and salt concentration stock<-matrix(nrow=8,ncol=3) colnames(stock)<-c("peg","ph","salt") stock[,1]<-rep(c(6,16),4) stock[,2]<-rep(c(8,8,9.5,9.5),2) stock[,3]<-rep(c(0,300),each=4) stock<-data.frame(stock) dim<-list(5:0/5,3:0/3,3:0/3) # the dilution serial of stock1 #call the function and return a new object test8vertex<-design8vertex(900,stock,dim) Design8Vertex-class Class "Design8Vertex" Design Class contains the info for 8-Vertex setting of crystallization matrix Objects from the Class Slots Extends Objects can be created by calls of the form new("design8vertex",...). volume: Object of class "numeric" the volume of each well in matrix block stock: Object of class "data.frame" stock composition portion: Object of class "array" portion of each stock in each well Class "Design", directly. Note writetecan signature(object = "Design8Vertex", filename = "ANY", source = "ANY", destination = "ANY", l... writetecan signature(object = "Design8Vertex", filename = "ANY", source = "ANY", destination = "ANY", l... preferred constructor design8vertex
6 6 Exp-class See Also design8vertex Design showclass("design8vertex") Exp-class Class "Exp" Store of experiment info of screen matrix and crystal score Objects from the Class Objects can be created by calls of the form new("exp",...). Slots screen: Object of class "Screen" the screen condition score: Object of class "numeric" score of crystal quality in each condition getoptimal signature(zga = "Exp"):... See Also getoptimal showclass("exp")
7 getcondition 7 getcondition Getter of the condition matrix in Screen object Getter of the condition matrix in Screen object getcondition(object) Value object matrix of screen condition # set up a Design object # please read the design8vertex for detail stock=matrix(nrow=8,ncol=3) colnames(stock)=c("peg","ph","salt") stock[,1]=rep(c(6,16),4) stock[,2]=rep(c(8,8,9.5,9.5),2) stock[,3]=rep(c(0,300),each=4) stock=data.frame(stock) dim=list(5:0/5,3:0/3,3:0/3) test8vertex=design8vertex(900,stock,dim) # construct a new Screen object testscreen<-design2screen(test8vertex) condition<-getcondition(testscreen) getcondition-methods ~~ for Function getcondition ~~ ~~ for function getcondition ~~ signature(object = "Screen")
![stock[,2]=rep(c(8,8,9.5,9.5),2) stock[,3]=rep(c(0,300),each=4) stock=data.](/docs-images/51/14094793/images/page_7.jpg "frame(stock) dim=list(5:0/5,3:0/3,3:0/3) test8vertex=design8vertex(900,stock,dim) # construct a new Screen object testscreen<-design2screen(test8vertex)")
8 8 getoptimal getoptimal get Optimal condition in the crystallization plate local regression for the crystal score across the screen matrix, and return the condition with the highest score getoptimal(zga) zga Exp object of experiment containing screen setting and score results # set up a Design object # please read the design8vertex for detail stock=matrix(nrow=8,ncol=3) colnames(stock)=c("peg","ph","salt") stock[,1]=rep(c(6,16),4) stock[,2]=rep(c(8,8,9.5,9.5),2) stock[,3]=rep(c(0,300),each=4) stock=data.frame(stock) dim=list(5:0/5,3:0/3,3:0/3) test8vertex=design8vertex(900,stock,dim) # set up a Screen object # please read the design2screen for detail testscreen<-design2screen(test8vertex) # the score from evaluation of crystal quality in screen plate # in this example, the crystals are scored according to # the scale proposed by Carter & Carter score=c(2,2,1,1,1,1,1,2,3,3,2,2,1,1,4,4,4,4,1,4,5,3,3,3,2,2,2,2,2,3,1,2,4,3,3,2,1,1, 1,1,1,1,1,1,3,4,3,4,2,2,4,3,3,3,1,4,3,3,4,2,1,2,3,3,4,3,1,3,3,3,5,4,2,2,2,3, 4,3,2,2,5,4,5,5,2,2,5,5,5,5,2,2,5,5,5,4) testexp=new(class= Exp,screen=testScreen, score=score) testopt<-getoptimal(testexp)
![colnames(stock)=c("peg","ph","salt") stock[,1]=rep(c(6,16),4) stock[,2]=rep(c(8,8,9.5,9.5),2) stock[,3]=rep(c(0,300),each=4) stock=data.](/docs-images/51/14094793/images/page_8.jpg "frame(stock) dim=list(5:0/5,3:0/3,3:0/3) test8vertex=design8vertex(900,stock,dim) # set up a Screen object # please read the design2screen for detail testscreen<-design2screen(test8vertex) # the")
9 getoptimal-methods 9 getoptimal-methods ~~ for Function getoptimal ~~ ~~ for function getoptimal ~~ signature(zga = "Exp") screen Screen constructor constructor of Screen object screen(fac, condition, position) fac condition position
10 10 screencsv Screen-class Class "Screen" Class for screen matrix Objects from the Class Objects can be created by calls of the form new("screen",...). Slots fac: Object of class "character" ~~ condition: Object of class "matrix" ~~ position: Object of class "matrix" ~~ getcondition signature(object = "Screen"):... screencsv signature(object = "Screen", filename = "character"):... See Also screencsv showclass("screen") screencsv csv exporter of Screen write Screen condition matrix into csv file screencsv(object, filename)
11 screencsv-methods 11 object filename Screen class charactor string of csv file # set up a Design object # please read the design8vertex for detail stock=matrix(nrow=8,ncol=3) colnames(stock)=c("peg","ph","salt") stock[,1]=rep(c(6,16),4) stock[,2]=rep(c(8,8,9.5,9.5),2) stock[,3]=rep(c(0,300),each=4) stock=data.frame(stock) dim=list(5:0/5,3:0/3,3:0/3) test8vertex=design8vertex(900,stock,dim) # construct a new Screen object testscreen<-design2screen(test8vertex) screencsv(testscreen,filename="opt.csv") screencsv-methods ~~ for Function screencsv ~~ ~~ for function screencsv ~~ signature(object = "Screen", filename = "character") writetecan Tecan worklist writer calculate the parameter for the Tecan Robot from Design object, out put a worklist file in csv format writetecan(object, filename, source, destination, liquidtype)
12 12 writetecan-methods object filename source destination liquidtype Design class character string of output worklist character string of source name, default Source1 (15ml tube rack) character string of destination name, default Destination (96-well deep block) vector of charactor of liquid type Details if no liquidtype is provided for the stock solution, the default will be set to B Note This method has polymorphism. If the liquidtype is missing for input, it will take it as B as Buffer for granted # set up a Design object # please read the design8vertex for detail stock=matrix(nrow=8,ncol=3) colnames(stock)=c("peg","ph","salt") stock[,1]=rep(c(6,16),4) stock[,2]=rep(c(8,8,9.5,9.5),2) stock[,3]=rep(c(0,300),each=4) stock=data.frame(stock) dim=list(5:0/5,3:0/3,3:0/3) test8vertex=design8vertex(900,stock,dim) writetecan(test8vertex,"testtecan_defaultliquid.csv","source1", Destination ) liquidtype=rep(c( B, P ),4) writetecan(test8vertex,"testtecan_setliquid.csv","source1", Destination,liquidType=liquidType) writetecan-methods ~~ for Function writetecan ~~ ~~ for function writetecan ~~ signature(object = "Design8Vertex", filename = "ANY", source = "ANY", destination = "ANY", liquidtyp signature(object = "Design8Vertex", filename = "ANY", source = "ANY", destination = "ANY", liquidtyp
13 Index Topic classes Design-class, 2 Design8Vertex-class, 5 Exp-class, 6 Screen-class, 10 Topic methods design2screen-methods, 4 getcondition-methods, 7 getoptimal-methods, 9 screencsv-methods, 11 writetecan-methods, 12 Topic package xtal-package, 2 screencsv,screen,character-method (screencsv-methods), 11 screencsv-methods, 11 writetecan, 11 writetecan,design8vertex,any,any,any,any-method (writetecan-methods), 12 writetecan,design8vertex,any,any,any,missing-method (writetecan-methods), 12 writetecan-methods, 12 xtal (xtal-package), 2 xtal-package, 2 Design, 5, 6 Design-class, 2 design2screen, 3 design2screen,design-method (design2screen-methods), 4 design2screen-methods, 4 Design8Vertex, 3 Design8Vertex (design8vertex), 4 design8vertex, 4, 6 Design8Vertex-class, 5 Exp-class, 6 getcondition, 7 getcondition,screen-method (getcondition-methods), 7 getcondition-methods, 7 getoptimal, 6, 8 getoptimal,exp-method (getoptimal-methods), 9 getoptimal-methods, 9 Screen (design2screen), 3 screen, 9 Screen-class, 10 screencsv, 10, 10 13
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