similar to: Fastest way to do HWE.exact test on 100K SNP data?

Displaying 20 results from an estimated 400 matches similar to: "Fastest way to do HWE.exact test on 100K SNP data?"

2008 Aug 22
2
help needed for HWE.exact in library "genetics"
Hi, I have a genotype data for both case and controls and would like to calculate the HW p-value. However, since the number of one genotype is 0, I got wired result. Would someone help me to figure it out? Or confirm it's right? Thanks a lot. ============ > library( "genetics" ) NOTE: THIS PACKAGE IS NOW OBSOLETE. The R-Genetics project has developed an set of enhanced
2009 Oct 16
1
How odds ratio is computed in fisher.test()?
I'm wondering how odds ratio is computed. I thought that it is (n11/n12)/(n21/n22), but it is not what fisher.test() computes. Could somebody let me know? > n11=3 > n12=1 > n21=1 > n22=3 > > n1_=n11+n12 > n2_=n21+n22 > > n_1=n11+n21 > n_2=n12+n22 > > x=rbind(c(n11,n12),c(n21,n22)) > > threshold=dhyper(n11,n1_,n2_,n_1) >
2004 Apr 19
11
Size of R user base
I have been trying to determine the size of the R user base, and was asked to share my findings with this mailing list. Although I still don't have any definite estimate of this number, I do have some interesting and indicative information: 1. It appears that there are about 100,000 S-PLUS users. Rationale: According to Insightful's 2002 Annual Report, over 100,000 people use
2012 Oct 15
1
library(rmeta)
Hello, I have a data with following format:      Predictors          n11     n12     n21     n22     Odds.Ratio    log.ratio    se.log.odds. 1 ProcOR respirato     2 ProcVaric vein      3 DiagCardiac anom   4 DiagAllergy        5  DiagOth skin dx    6    DiagGastritis          I want to plot odds ratio by command: forestplot in rmeta library, but I get the following error constantly.  Error in
2012 Nov 12
1
reshape
Hi, I have a R output that looks as follow: Rad:0 Rad1:2 Rad3:3 I want to make a new matrix that looks like : sample size is 2400 Variable    n11  n12 Rad            0     2400-0=2400 Rad1          2       2400-2 Rad3  3      2400-3   Thanks a lot for your time and help:) Best,Farnoosh Sheikhi [[alternative HTML version deleted]]
2011 Oct 08
1
HWEBayes, swapping the homozygotes genotype frequencies
I evaluated the Bayes factor in the k=2 allele case with a "triangular" prior under the null as in the example in the help file: HWETriangBF2(nvec=c(88,10,2)) [1] 0.4580336 When I swap the n11 entry and n22 entry of nvec, I received totally different Bayes factor: > > HWETriangBF2(nvec=c(2,10,88)) [1] 5.710153 > In my understanding, defining the genotype frequency as
2002 May 21
2
using axis with newline characters
Wondering if I missed anything or if that's a problem with R: I want to have many x axis tickmarks and labels such that it makes sense to put them on multiple "lines". The newline character seems to be ignored though for axis labels: plot(1:33, axes=F) axis(1, 9, 9) axis(1, 11, "\n11") axis(1) # whereas title("one\ntwo") works as I expect it to work. In
2007 Nov 30
0
Is there any multivariate regression function to combine all variables from a dataset?
Hi everybody, I've been looking for a function that combines all variables from a dataset because I need to do multivariate regression. If we have linear regression with an expression like f(x) = a0 + sum(ai*xi) what I want to do is something like f(x) = a0 + sum(ai*xi) + sum(sum(bij * xi * xj)) + sum(sum(sum(cijk*xi*xj*xk))) + ... So I need a function that combines all the values from
2010 May 13
1
Comparing histograms?
Rhelpers: I'm curious what the appropriate analysis to use for testing the hypothesis that two histograms are statistically different from one another? Thanks! --j
2003 Aug 30
3
fisher.test() gives wrong confidence interval (PR#4019)
The problem occurs when the sample odds ratio is Inf, such as in the following example. Given the fact that both upper bounds of the two 95% confidence intervals are Inf, I would have expected that the two lower bounds be equal, but they aren't. x <- matrix(c(9,4,0,2),2,2) x # [,1] [,2] #[1,] 9 0 #[2,] 4 2 rbind("two.sided.95CI"=fisher.test(x)$conf.int,
2005 Apr 05
2
cat bailing out in a for loop
Dear All, I am trying to calculate the Hardy-Weinberg Equilibrium p-value for 42 SNPs. I am using the function HWE.exact from the package "genetics". In order not to do a lot of coding "by hand", I have a for loop that goes through each column (each column is one SNP) and gives me the p.value for HWE.exact. Unfortunately some SNP have reached fixation and HWE.exact requires a
2011 Sep 12
14
[Bug 8450] New: --link-dest seems not to work mounted NTFS file systems
https://bugzilla.samba.org/show_bug.cgi?id=8450 Summary: --link-dest seems not to work mounted NTFS file systems Product: rsync Version: 3.0.8 Platform: x86 OS/Version: Linux Status: NEW Severity: normal Priority: P5 Component: core AssignedTo: wayned at samba.org
2013 Jun 24
1
help needed with printing multiple arguments as vectors, not matrices
** I am using the following way to get p-values from fiser exact test. However, I do need to print for each pair the values "n00, n01, n10, n11". How can I print that as a table and not a matrix as below along with the p-value? Any help will be greatly appreciated fish <- function(y, x) {n00 = sum((1-x)*(1-y)); n01 = sum((1-x)*y); n10 = sum(x*(1-y)); n11 = sum(x*y); a =
2020 Oct 09
1
Aide pour finaliser ce code
Hello. Here is my R code. I used the functional data . Now I need to use the functional data by applying the kernels instead of the xi, yi functions. Bonjour. Voici mon code en R . J'ai utiliser les donn?es fonctionnelles . Maintenant j'ai besoin d'utiliser les donn?es fonctionnelles en appliquant les noyaux ? la place des fontions xi, yi library(MASS)
2020 Oct 13
1
Please need help to finalize my code
Hm. Google tells me that kernel function is in stats package which comes with base installation and is invoked when you start R. search() [1] ".GlobalEnv" "package:stats" "package:graphics" [4] "package:grDevices" "package:utils" "package:datasets" [7] "package:methods" "Autoloads"
2020 Oct 10
3
Please need help to finalize my code
Good evening dear administrators, It is with pleasure that I am writing to you to ask for help to finalize my R programming algorithm. Indeed, I attach this note to my code which deals with a case of independence test statistic . My request is to introduce the kernels using the functional data for this same code that I am sending you. So I list the lines for which we need to introduce the
2020 Oct 13
0
Please need help to finalize my code
What do you *mean* "when you want to use the kernels". WHICH kernels? Use to do WHAT? In your browser, visit cran.r-project.org then select "Packages" from the list on the left. Then pick the alphabetic list. Now search for 'kernel'. You will find dozens of matches. On Wed, 14 Oct 2020 at 05:15, PIKAL Petr <petr.pikal at precheza.cz> wrote: > Hm. Google tells
2012 Nov 13
4
for loop
HI, You can do this in many ways: dat1<-read.table(text=" med1,med2,med3???? ?1,0,1?????? 0,1,1??? 2,0,0 ",sep=",",header=TRUE)?? #1st method library(reshape) dat2<-melt(dat1) dat3<-aggregate(dat2$value,by=list(dat2$variable),sum) ?colnames(dat3)<-c("name","sum(n11)") ?dat3 #? name sum(n11) #1 med1??????? 3 #2 med2??????? 1 #3 med3??????? 2
2011 Apr 16
0
Question abt power calculation in multistrata data using Hmisc or other package
Hi, I have two unequal patient groups belonging to different geographic locations, treated by different drug regimens and their survival data. N1=150 and N2=60 In each group of data there are three strata for one independent variable- treatment status (2=two drugs administered, 1=only one conventionally used drug administered, 0=no drug administered), dead or not and months to death. In order to
2013 Dec 18
1
Fwd: Bad \usage lines question
Dear colleagues, In checking a function I am adding to an R package, I get the following warning pair: ... Bad \usage lines found in documentation object 'nominal': "\\method{print}{nominal}"(x, max.print = 10, posthoc = "std.pearson.residuals.sign", assoc = ifelse("univariate" list(c("N", "alpha.X2",