search for: al2

Thank you for the suggestion, Bill. The result is not quite what I would like. Here's sample code for you or anyone else who may be interested: Al1 = c('A','C','C','C') Al2 = c('G','G','G','T') Freq1 = c(0.0078,0.0567,0.9434,0.9908) MAF = c(0.0078,0.0567,0.0566,0.0092) m1 = data.frame(Al1=Al1, Al2=Al2,Freq1=Freq1,MAF=MAF,major_allele='') m1 Al1 Al2 Freq1 MAF major_allele 1 A G 0.0078 0.0078 2 C G 0.056...

Hello, All! How might one accomplish this using the by() function? m1 is a data frame. # populate column "m1$major_allele" for ( i in 1:length(m1$major_allele)) { if ( m1$Freq1[i] == m1$MAF[i]){ m1$major_allele[i] = m1$Al1[i] } else{ m1$major_allele[i] = m1$Al2[i] } } Jim [[alternative HTML version deleted]]

...ct number of dimensions". However gen is 1000x200 (ind x loc) and so is g could anybody help me for (i in 1 : loc) { #loc=200 for (j in 1 : ind) { #ind=1000 g1 <= function ( gen ) matrix ( if (gen[j, i] == 0) al1 [i, 1] + al1 [i, 1] else if (gen [j, i] == 1) al1 [i, 1] + al2 [i, 1] else if (gen [j, i] == 2) al2 [i, 1] + al2 [i, 1] else 999, ncol = loc, nrow = ind) g2 <= function ( gen ) sample (b1, 1, re = T) #b1 is 1x3 and came from a vector 1000X1 (e.g b1 <- c(x [1000,1]...) xx <= if (runif (1) >= (1 - r2)) g1 else g2 g [j, i] <= xx (gen [j,...

Hey, I have a dataset and I want to identify the records by groups for further use in ggplot. Here is a sample data: ID Value AL1 1 AL2 2 CA1 3 CA4 4 I want to identify all the records that in the same state (AL1 AND A2), group them as "AL", and do the same for CA1 and CA4. How can I have an output like: ID Value State AL1 1 AL AL2 2 AL CA1 3 CA CA4 4 CA Thanks for your help! [[alternative...

Is there a way to combine two columns within a data frame? Example data: id snp AL1 AL2 1500 30 A B 1510 30 A A 1520 30 A B This is what I would like: indv snp AL1AL2 1500 30 AB 1510 30 AA 1520 30 AB Any help is greatly appreciated. Alysta

...udinal Data Analysis. Oxford University Press, 2003" using R. I have the SAS code and S-Plus code from the UCLA site (doesn't include chapter 8 or later problems). In chapter 8, there is a structural equation/path model which can be specified for the sem package as follows S <- cov(al2) #al2 contains the variables alc1, alc2, alc3, and cons N <- 1122 modelA.ram <- specify.model() f1 -> alc1, NA, 1 f1 -> alc2, NA, 1 f1 -> alc3, NA, 1 f2 -> alc1, NA, 0 f2 -> alc2, NA, .75 f2 -> alc3, NA, 1.75 cons -> f1, p0...

...riable with possible values between 0 and 1 - mine runs from 0.05 to 0.5, increasing with steps of 0.05 s.size - a count variable - increases from 3 to 25 with steps of 1, and from 25 to 60 with steps of 5 Each combination of s.size and bedekking has 100 repeats so the resulting dataframe 'dat.al2' consists of 30000 observations of 3 variables. Because the response variable has values between 0 and 1, I used a logistic GLM: > gmodel <- glm(R.AUC ~ bedekking + s.size, data=dat.al2, family = quasibinomial(link=logit)) R.AUC increases with increasing s.size and decreasing bedekking...

...alX[1], specialX, specialX[length(specialX )]), c(0, specialY, 0), density=c(-110),col="lightgray" ) shadedArea <- round(pnorm(mu - 1.96 * sigma, mean=mu, sd=sigma),4) ### I want to insert annotation about area on left side. al1 <- bquote(Prob(x <= .(round(criticalValue,2)))) al2 <- bquote(phantom(0) == F( .(round(criticalValue,2)) )) al3 <- bquote(phantom(0) == .(round(shadedArea,3))) ### Hard to position this text "just right" ### Have tried many ideas, this may be least bad. ### Get center position in shaded area medX <- median(specialX) ### density a...

I want to shade the area under the curve of the standard normal density. Specifically color to the left of -2 and on. How might i go about doing this? Thanks -- View this message in context: http://n4.nabble.com/Shade-area-under-curve-tp1586439p1586439.html Sent from the R help mailing list archive at Nabble.com.

Hello All, I have a toy dataframe like this. It has 8 columns separated by tab. Name SampleID Al1 Al2 X Y R Th rs191191 A1 A B 0.999 0.09 0.78 0.090 abc928291 A1 B J 0.3838 0.3839 0.028 0.888 abcnab A1 H K 0.3939 0.939 0.3939 0.77 rx82922 B1 J K 0.3838 0.393 0.393 0.00 rcn393...

...want to pass only some of them to a function, e.g. glm(resp~from PC1 to PC10, PC15, etc.,...) is there a faster way than simply writing each variable name in the formula? 2) Again, I have a dataframe, say ali.df, with tha following variables: ali1, ali2, ...ali78 I want to sum, for example, ali1+al2+ali7+f rom ali10 to ali20 etc., then from ali4 to ali8, etc. and then put everything in a new dataframe I'd do somthing like: new.df <- cbind(apply(ali.df[c(1:2,7,10:20)],1,sum), apply(ali.df[4:8],1,sum)) and so on. Is it the right and only way? Thanks in advance (and forgive my orrib...

...much as possible: one of my datasets looks like this(apologies if the formatting gets weird): foresttype region crosstype experiment linelabel yproductivity l g wx 1 al1 63 l g wx 1 al2 26 ... and so on. Each horizontal line refers to a single observation. The first horizontal line, for example, refers to a single cross that was found to have a yproductivity value of "63", and that cross happened to be in the "l" foresttype, the "g" re...

...by first minimising glm(resp~ var1 + var2, family=binomial, data=data)$deviance where var1= exp(-a1*dist1), and var2= exp(-a2*dist2), where a1 and a2 are parameters and dist1 and dist2 are independent variables. Next, I calculate the value of var1 (and var2) by plugging in the value of al1 (and al2) that minimises deviance, and fit glm(resp~ var1+var2 , family=binomial, data=data) Var1 in this model thus includes two parameters - the standard glm() coefficient and a1. This is (of course) not recognized by drop1(). Usually I extract a rough p-value for var1 in this model by 1-pchisq(scaled...

...don't know how much of a reduction I can expect at the moment. I'm not sure I fully understand the super-resource suggestion. I've attached my WIP so you can take a look at the code in context but the relevant extracts are below. def P5600IssueALU : ProcResource<1>; def P5600IssueAL2 : ProcResource<1>; def P5600ALQ : ProcResGroup<[P5600IssueALU]> { let BufferSize = 16; } def P5600AGQ : ProcResGroup<[P5600IssueAL2, ...]> { let BufferSize = 16; } def P5600WriteALU : SchedWriteRes<[P5600IssueALU]>; def P5600WriteAL2 : SchedWriteRes<[P5600IssueAL2]>;...

...+pqo1/tBX0XCPFH0VST6KhJ9TfRN1PsiPcen1XWaqTyAT3WddvGEeORrY7YrUJ5uay/Rk3eC y742+wBeSPZSAq4nLLjQsgJEXueX5ZcJE/aUMCWKu66Yyb52giv7ANsbM9mgTnaXk3fZ8o7lZPfP r4z+OvBAtWy5WIoo9grdjz5w8ePaqrJjGVG1OmxmtVqK24tOkwnaxsoAdOMv6xIS/Ph4iSqHQzle OEpSv6PQFQtdXFzM8T9zQR8T1IjOfrxoHOxivhy2jDoCkppTXcNxFNTMRhhw53EAr0viT6IjgAl2 4Iq743JrYh5eikqEKXdchmXLY1wsDstiVHcVVTouh+NyU14RJfp/cyrEIwplbmRzdHJlYW0KZW5k b2JqCjM5IDAgb2JqCjUxMDgKZW5kb2JqCjQwIDAgb2JqCjw8IC9UeXBlIC9Gb250RGVzY3JpcHRv ciAvQXNjZW50IDkwNSAvQ2FwSGVpZ2h0IDcyMyAvRGVzY2VudCAtMjEyIC9GbGFncyAzMgovRm9u dEJCb3ggWy02NjUgLTMyNSAyMDI4IDEwMDZdIC9Gb250TmFtZSAvRFVWRUtVK0FyaWFs...