similar to: liner regression for multiple keys

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

is it possible to map 2 plots(c and d) in a single output plot? library(ggplot2) c <- ggplot(mtcars, aes(qsec, wt)) d <- ggplot (mtcars, aes(qsec, wt)) c + stat_smooth(fill="darkgrey", colour="blue", size=2, alpha = 0.2) d + stat_smooth(fill="darkgrey", colour="red", size=2, alpha = 0.2) -- View this message in context:

Dear list, I want to retrieve the p-value of a two-polynomial regression. For a one-polynomial lm I can easily do this with: summary(lm(b~a, data=c)[[4]][[8]]. But how do I find the final p-value in the two-polynomial regression? Under $coefficients I don't find it Any suggestions? Patrick alt <-(2260,2183,2189,1930,2435, 2000,2100,2050,2020,2470, 1700,2310,2090,1560,2060,

OK, what is the trick to extracting the overall p value from an lm object? It shows up in the summary(lm(model)) output but I can't seem to extract it: > test2 = apply(aa, 1, function(x) summary(lm(x[,1] ~ 0 + x[,3] + x[,6]))) > test2[[1]] Call: lm(formula = x[, 1] ~ 0 + x[, 3] + x[, 6]) [omitted summary output] F-statistic: 40.94 on 2 and 7 DF, p-value: 0.0001371 It does not seem

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 =

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) {

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

[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 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:

Dear useRs, i have vectors of about 27 descriptors, each having 703 elements. what i want to do is the following 1. i want to do regression analysis of these 27 vectors individually, against a dependent vector, say B, having same number of elements.2. i would like to know best 10 regression results, if i do regression analysis of dependent vector against the random combination of any 4

Dear R users I have run an regression and want to extract the p value of the F statistics, but I can find a way to do that. x<-summary(lm(log(RV2)~log(IV.m),data=b)) Call: lm(formula = log(RV2) ~ log(IV.m), data = b[[11]]) Residuals: Min 1Q Median 3Q Max -0.26511 -0.09718 -0.01326 0.11095 0.29777 Coefficients: Estimate Std. Error t value Pr(>|t|)

Hi, I'm trying to get the p-value from the 'lm' regression function as a list object. For example, I can get r^2 from the following code by entering summary(fm)$r.squared. Is there a way to get the p-value? If not, is there a function where I can enter the f-value and degrees of freedom to get the p-value? Thanks. x <- c(1,2,3,4,5,6,7,8,9,10) y <- c(1,2,3,4,4,5,6,8,1,9) fm

Dear Sir or Madam, I am a student at MSc Probability and Finance at Paris 6 University/ Ecole Polytechnique. I am using R and I can't find an answer to the following question. I will be very thankful if you can answer it. I have two vectors rendements_CAC40 and rendements_AlcatelLucent. I use the lm function as follows, and then the sumarry function: regression=lm(rendements_CAC40 ~

Hello, Thank you very much for looking at this. I have a "seasonal" user for R. I teach my undergrads and graduates students statistics using R and often find myself trying to solve problems to process student collected data in an efficient way. In this case, I have a data.frame with multiple observations. These are gas concentrations in a chamber and are used to measure into rates,

Hi guys I have an input file with multiple columns and and rows. Is it possible to calculate correlation of certain value of certain No (For example x of S1 = 112) with all other values (for example start with x 112 corr a 3 of S1 = x-a 0.2 ) INPUT ******* No S1 S2 S3 S4 Sn a 3 4 45 34 23 x 112 0 12 23 0 b 0 1 23 12 1 n 0 1 0 1 1

I am trying to deduce the one liner for an rpm I am packaging to edit a php configuration file from within my spec. The line I am editing looks like: $conf['nagios_base'] = "/nagios/cgi-bin"; What are the escape requirements Perl needs from within the shell to search for this? As I have seen, the syntax is a mess, any pointers would be appreciated! thanks, jlc

Hi, I would like to write a one-line R code to create a 3-dim array, B, of dimension (n,n,m) from a matrix, A, of dimension (m,n) such that the i-th element of the 3-dim array, B[, , i] is the outer product of the i-th row of A. Thanks for any help, Ravi. [[alternative HTML version deleted]]

Hi, I have a line such as: myline <- " 0.100000 1.5000 0.6000 538 0.369404" and I would like to put the numbers into a vector. Some combination of tabs and spaces occur between the numbers. I tried: try1 <- strsplit(myline,"[[:blank:]]+") > try1 [[1]] [1] "" "0.100000" "1.5000"

This awk command pulls URLs from an apache config file, where $x is the config filename. awk '/:8008\/root/ {printf $3 "\t"}' $x The URL that is output by the script looks something like this: ajpv12://hostname.network.company.com:8008/root Is there a way to alter the output so it only shows "hostname" by itself? Do I need to pipe this through awk again to clean it

Dear Sir/Madam, I have two vectors say x<-c(0,0,2.73,3.42,3.95,4.26) and y<-c(0.0,0.5,1.20,1.90,2.6,3.3). I want to fit y as a function of x and get the equation.Do I have to use glm() ? Rangesh [[alternative HTML version deleted]]