similar to: small change in output

inputfille snpid indid genotype gvariable probeid gene geneexpression rs1040480 CHB_NA18524 C/T 2 GI_19743926-I PTPRT 5.850586 rs1040480 CHB_NA18526 C/C 1 GI_19743926-I PTPRT 6.028641 rs1040480 CHB_NA18529 C/C 3 GI_19743926-I PTPRT 5.944392 rs1040481 CHB_NA18532 C/C 1 GI_19743926-I PTPRT 5.938578 rs1040481 CHB_NA18537 C/C 2 GI_19743926-I PTPRT 5.874439 rs1040481 CHB_NA18540 C/C 3 GI_19743926-I

a1 is the first key in input. second column is x-axis and 3rd is y-axis and 4th is its corresponding key. Now for every key in 1st column I would like to calculate LR that gives p value. I tried to manage with a single key. But my problem is that How could I manage multiple keys in input. Thanx in advance input a1 1 2.5 x a1 2 3.5 x a1 3 4.5 x a1 1 2.6 x a1 2 3.8 x b1 1 4.6 y

[Please use the subject line!] In the help page for summary.lm, the "Value" section says that the returned object has a component called "fstatistic", which has the F-statistic and the associated numerator and denominator degrees of freedom. You can get the p-value by something like: fstat <- summary(speciallinearmodel)$fstatistic pval <- pf(fstat[1], fstat[2],

Hi List, My goal is to force R not to print in scientific notation in the sixth column (rel_diff - for the p-value) of my data frame (not a matrix). I have used the format.pval () and printCoefmat () functions on the data frame. The R script is appended below. This issue is that use of the format.pval () and printCoefmat () functions on the data frame gives me the desired results, but coerces

Hello, I am using fdrtool(x, statistic="pvalue") where x is a vector of chisq p-values. I can get this command to work with some x, but not with others. When it does NOT work, I get the following screen output: > fdrtool(pvals$Chi2.pval, statistic="pvalue") Step 1... determine cutoff point Step 2... estimate parameters of null distribution and eta0 Step 3... compute p-values

Hi all, Just a minor issue that I am not sure whether this is considered a "bug." It is about the help page. In the help page of printCoefmat(), for the argument 'eps.Pvalue', the description is as below: number, .. I have to read the source to figure out that this argument is to be used by format.pval(). Maybe the description of 'eps.Pvalue' can be revised to refer

On 29/10/2023 3:48 a.m., Shu Fai Cheung wrote: > Hi all, > > Just a minor issue that I am not sure whether this is considered a > "bug." It is about the help page. > > In the help page of printCoefmat(), for the argument 'eps.Pvalue', the > description is as below: > > number, .. > > I have to read the source to figure out that this argument

** 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 =

Hi, A following function was kindly provided by GGally?s maintainer, Barret Schloerke. function(data, mapping, ...) { p <- ggplot(data = data, mapping = mapping) + geom_point(color = I("blue")) + geom_smooth(method = "lm", color = I("black"), ...) + theme_blank() + theme(panel.border=element_rect(fill=NA, linetype =

Dear all, I am not fluent in R and am struggling to 1) apply a lm to a weight-size dataset, thus the model has to run separately for each species, each year; 2) extract coefs, r-squared, n, etc. The data look like this: year sps cm w 2009 50 16 22 2009 50 17 42 2009 50 18 45 2009 51 15 45 2009 51 16 53 2009 51 17 73 2010 50 15 22 2010 50 16 41 2010 50 16 21 2010

Hi, I am trying to run the command "forward.sel.par," however I receive the error message: "Error: could not find function 'simpleRDA2'." I have the vegan library loaded. The documentation on "varpart" has not helped me to understand why I cannot call this function. Maybe I am missing something obvious because I am still an 'R' novice. Below is a

Hi r-helpers! I need to save the output of summary() function that I?ve runned like this: z<- lmList(y~x1+x2| x3, na.action=na.omit,data1,subset=year==1999) w<-summary(z) The output (w) is something like this: Call: Model: y ~ x1 + x2 | x3 Data: data1 Coefficients: (Intercept) Estimate Std. Error t value Pr(>|t|) 1 0.081110514 1.141352e-01

Sorry, I pasted the wrong file in earlier... this is the correct one: pValCalculator(b, n=20, m=20) { ind <- 1:min(c(n,m)) prob <- (1-pnorm(b,sd=std*sqrt(ind))) prob1 <- sum((n-ind+1)*(m-ind+1)*prob) prob1 } inputData <- scan("/users/lvssso/projects/LAMA/output/pValLamaScore.tmp", list(block1 = "",block2 = "",width1 = 0,width2 = 0,alignment = 0,score

Hi there, I am stuck trying to solve what should be a fairly easy problem. I have a data frame that essentially consists of (ID, time as seqMonth, variable, value) and i want to find the regression coefficient of value vs time for each combination of ID and Variable. I have tried several approaches and none of them seems to work as i expected. For example, i have tried:

Hi, Sorry to bother you guys with this syntax problem, this is my first R program, and I seem to not have grasped something right. I keep getting an error message from 'parse' on the line with the *** : pValCalculator(b, n=20, m=20) { ind <- 1:min(c(n,m)) prob <- (1-pnorm(b,sd=std*sqrt(ind))) prob1 <- sum((n-ind+1)*(m-ind+1)*prob) prob1 } inputData <-

Hi, I am new to R. and even though I've made my code to run and do what it needs to . It is taking forever and I can't use it like this. I was wondering if you could help me find ways to fix the code to run faster. Here are my codes.. the data set is a bunch of 0s and 1s in a data.frame. What I am doing is this. I pick a column and make up a new column Y with values associated with that

Hello, in R-2.1.0 I'm trying to prodice trellis plots from an lmList object as described in the help for plot.lmList. I can generate the plots from the help, but on my own data plotting fails with an error message that I cannot interpret (please see below). Any hints are greatly appreciapted. kind regards, Arne > dim(d) [1] 575 4 > d[1:3,] Level_of_Expression SSPos1 SSPos19

Hello R-Help, ----------------------------------------------------------------------------------------------------------------------------------------- Issues (there are 2): 1) Possible bug when using lmtest::encomptest() with a linear model created using nlme::lmList() 2) Possible modification to lmtest::encomptest() to fix confusing fail when models provided are, in fact, nested. I have

Sent this mail in rich text format before. Excuse me for this. ------------------------ Dear all, I'm using the lrm function from the package "Design", and I want to extract the p-values from the results of that function. Given an lrm object constructed as follows : fit <- lrm(Y~(X1+X2+X3+X4+X5+X6+X7)^2, data=dataset) I need the p-values for the coefficients printed by calling

could someone explain why the name of FPVAL gets " .value" concatenated onto it when the code below is run and temp is returned. I've been trying to figure this out for too long. It doesn't matter when I put the FPVAL in the return statement. It happens regardless of whether it's first or last. Thanks. f.lmmultenhanced <- function(response, pred1, pred2) {