Re: [R] two difficult loop

3933 in >sorted map$reg and only summing first 12 of them gives>0.85. Then my answer is going to be 12 for 29220 - 63933 in ref. Thanks I lot for your patience. Cheers, Greg On Sun, Jun 12, 2016 at 10:35 PM, greg holly <mak.hho...@gmail.com> wrote: > Hi Bert; > > I do

Re: [R] two difficult loop

you mention, but only the second will yield an > unique or tied value for all of the cases. So your result data frame > will have an unspecified number of values for each row in "ref" for > the first task. > > Jim > > > On Mon, Jun 13, 2016 at 6:14 AM, greg holly <m

[R] two difficult loop

Dear all; I have two data sets, data=map and data=ref). A small part of each data set are given below. Data map has more than 27 million and data ref has about 560 rows. Basically I need run two different task. My R codes for these task are given below but they do not work properly. I

Re: [R] two difficult loop

: In max(x) : no non-missing arguments to max; returning -Inf On Mon, Jun 13, 2016 at 10:28 AM, greg holly <mak.hho...@gmail.com> wrote: > Hi Jim; > > I do apologize if bothering. I have run on the real data and here is the > error message I got: > > Thanks, > > Greg >

Re: [R] two difficult loop

nce of integers regrange[1]:regrange[2] is too long to > be allocated. Most likely this is because one or both of the endpoints > are infinite. Maybe if you can find where the NAs are you can fix it. > > Jim > > On Tue, Jun 14, 2016 at 12:29 AM, greg holly <mak.hho...@gmail.com> wr

[R] help for fine mappting

dear all; I am sorry for this posting. I have got help from Jim, Bert, Jeff and PIKAL on similar issue before. I tried to modify Jim`s code to the real data but it did not work. Now I am posting first two rows the imitation of real data using dput() format (please see at the bottom). I have two

[R] Fwd: help for fine mappting

Dear all; Unfortunately I did not get any response for my following questions. It is time sensitive job. I would be greatly appreciate if you give help soon. Regards, Greg I am sorry for this posting. I have got help from Jim, Bert, Jeff and PIKAL on similar issue before. I tried to

[R] (no subject)

Hi all; I am going to run models for variable selection using elastic-net. Because I have about 1500 descriptive (independent) variables which they are highly correlated. Before running elastic-net and even single regressions (~1500) I need get fitted values for dependent variables using MIXED

[R] Predicted values VS residuals

Dear all; I am sorry for my earlier post without subject. My question in earlier mail was: I am going to run models for variable selection using elastic-net. Because I have about 1500 descriptive (independent) variables which they are highly correlated. Before running elastic-net and even single

[R] looping problem

Hi all; I have 22 directories named chr1, chr2,,chr22. Each directory has a file named "Z-score.imputed". I would like to combine Z-score.imputed files into one. I wrote the following loop but did not get any results. Your helps are highly appreciated. regards, Greg temp<-c() for(i in

Re: [R] looping problem

<- rbind(temp, psT) > } > > str(temp) # to see what you have > > Hope this helps, > > Rui Barradas > > > > > Em 01-02-2017 17:25, greg holly escreveu: > >> Hi all; >> >> I have 22 directories named chr1, chr2,,chr22. Each directory has a &g

Re: [R] looping problem

on. Regards, Greg On Thu, Feb 2, 2017 at 9:39 AM, Rui Barradas <ruipbarra...@sapo.pt> wrote: > Hello, > > If I understand correctly, just use ?cbind. > > Rui Barradas > > Em 02-02-2017 13:33, greg holly escreveu: > >> Hi Rui; >> >> Is there any way to

Re: [R] looping problem

ginal Message- > > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of greg > holly > > Sent: Thursday, February 2, 2017 4:13 PM > > To: Rui Barradas <ruipbarra...@sapo.pt> > > Cc: r-help mailing list <r-help@r-project.org> > > Subject: Re: [R

Re: [R] looping problem

="") > psT<-read.table(infile,header=T,as.is=T,sep="\t") > temp <- rbind(temp, psT) > } > > str(temp) # to see what you have > > Hope this helps, > > Rui Barradas > > > > > Em 01-02-2017 17:25, greg holly escreveu: > >&g

[R] lines those not started with "rs"

Hi all; I have a file which has about 3.000.000 lines. Most of the lines at first column start with "rs", for example, rs1056, rs1076 and so on. I would like to get the lines which do not start with "rs" . Your helps highly appreciated. Regards, Greg [[alternative HTML version

Re: [R] lines those not started with "rs"

is a good tool but not > the tool I would use for this job. The tool I would > use is grep. The following command should get you want you want: > grep -v "^rs" > > Bob > > > On 1/30/2017 9:23 AM, greg holly wrote: > >> Hi all; >> >> I have a file

[R] ggplot

Dear all; I can not get legend position at the top when using the following code. It does give at the right. Your help is greatly appreciated. p3 <- ggplot(a, aes(x = SUPER.PATHWAY, y = SI)) + #theme_classic() theme_classic(legend.position="top",

[R] Error in Summary.factor(c(24L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, :

Dear all; I am getting the following error message when I run maSigPro package by using make.design.matrix commend. I could not figure out why this error happens. Thanks for your help Greg Error in Summary.factor(c(24L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, : ‘min’ not meaningful for

Re: [R] Error in Summary.factor(c(24L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, :

. des_blood=make.design.matrix(blood, degree=11) On Sat, Nov 12, 2016 at 7:54 PM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote: > On 12/11/2016 7:33 PM, greg holly wrote: > >> Dear all; >> >> I am getting the following error message when I ru

[R] CONFUSSING WITH select[!miss] <- 1:sum(!miss)

Dear All; I am very new in R and try to understand the logic for a program has been run sucessfully. Here select[!miss] <- 1:sum(!miss) par is confussing me. I need to understandand the logic behind this commend line. Thanks in advance for your help, Greg miss <-

Re: [R] CONFUSSING WITH select[!miss] <- 1:sum(!miss)

ALSE FALSE TRUE FALSE FALSE TRUE FALSE > # create a vector of zeros the length of the number of rows > select <- integer(nrow(ph)) > select > [1] 0 0 0 0 0 0 0 0 0 0 > # get the indices for the rows that do _not_ have NAs > select[!miss] <- 1:sum(!miss) > select >

Re: [R] heat maps with qplot

axis.title if y and x are to be identical, > or axis.text.x, axis.text.y, axis.title.x, axis.title.y if you need > different font size. > > HTH > Ulrik > > On Fri, 10 Mar 2017 at 15:47 greg holly <mak.hho...@gmail.com> wrote: > >> Hi all; >> >> The followings are my

[R] heat maps with qplot

Hi all; The followings are my R codes for heat maps in ggplot2. I need to specify the font size for the y-axis (x-axis works) as well as font size for label y and x too. Your help highly appreciated. Thanks, Greg qplot(x=Var1, y=Var2, data=melt(cor(a, use="p")), fill=value, geom="tile") +

[R] legend and values do not match in ggplot

I have following codes for ggplots. The legends are given in the plot do not match with the values specified in the codes given below. Your helps highly appreciated. Greg library(ggplot2) p <- ggplot(a,aes(x=NO_BMI_FI_beta ,y=FI_beta ,color= Super.Pathway))+ theme_bw()

[R] ggplot problem

Hi all; When I run the following program substantially I have "Warning message: position_dodge requires non-overlapping x intervals" How I can overcome this problem. Regards, Greg p <- ggplot() + geom_point(data=a, aes(x=Betas, y=Traits, color= Super.Pathway), shape=15, size=4) p <- p +

Re: [R] point size

geom_point.html > > ggplot(mydata, aes(x = X, y = log10_P)) + > theme_bw() + > theme(panel.border=element_blank(), legend.position="top", > axis.text=element_text(size = 8)) + > geom_point(aes(color = Traits, size = log10_P)) > > Jean > > On Fri, Jun 16, 2

[R] point size

Hi all; I am running the following ggplot codes. Runs well. However, I need to reflect the numeric values of the log10_P to the point size in the graph. Your help highly appreciated, Regards, Greg p <- ggplot(mydata, aes(x = X, y = log10_P)) + theme_bw()

[R] remove quotes from matrix

Hi all; I have data at 734*22 dimensions with rows and columns names are non-numeric.When I convert this data into matrix then all values show up with quotes. Then when I use x1= noquotes(x) to remove the quotes from the matrix then non-numeric row names remain all other values in matrix

Re: [R] remove quotes from matrix

dun...@gmail.com> wrote: > On 19/09/2017 9:47 AM, greg holly wrote: > >> Hi all; >> >> I have data at 734*22 dimensions with rows and columns names are >> non-numeric.When I convert this data into matrix then all values show up >> with quotes. Then when I use &g

Re: [R] remove quotes from matrix

ning", "Pyrimidine,_Uracil_containing", "Riboflavin", "Secondary_Bile_Acid", "Short_Chain_Fatty_Acid", "Sphingolipid", "Steroid", "Sterol", "TCA_Cycle", "Tocopherol", "Tryptophan", "Urea_cycle;_Arg

Re: [R] remove quotes from matrix

0.48610 0.70830 0.01337 > 5 Alanine_and_Aspartate -0.00982 0.32930 0.01597 -0.04353 > > dimnames(dm) > [[1]] > [1] "1" "2" "3" "4" "5" > > [[2]] > [1] "Sub_Pathways" "BMI_beta" "

[R] the first name of the first column

Dear all; I need to run heatmap. Because my first column in my data is alphanumeric, I can not run as.matrix(scale(my_data)). So I need to make my data readable as in data(mtcars). In *mtcars *data the first column is alphanumeric and has no name. Thanks, Greg [[alternative HTML

[R] par(mfrow=c(3,4)) problem

Hi all; I need to put 12 different plot2 into the same matrix. So my array for the matrix will be par(mfrow=c(3,4)). I am running ggplot2 to produce my 12 plots. For some reason, par(mfrow=c(3,4)) did not turn out 3*4 matrix. my basic R codes for each plot is par(mfrow=c(3,4)) library(ggplot2)

Re: [R] plotting the regression coefficients

> > Wild guess - did you try ggplot? > > Cheers > Petr > > > > -Original Message- > > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of greg > holly > > Sent: Thursday, February 8, 2018 8:14 AM > > To: r-help mailing list

[R] plotting the regression coefficients

Hi Dear all; I would like to create a plot for regression coefficients with each independent variable (x) along the side and the phenotypes (y) across the top (as given below). For each data point, direction and magnitude of effect could be color and significance could be the size of the circle?

Re: [R] plotting the regression coefficients

Rich > > > On Mon, Feb 12, 2018 at 3:49 AM, PIKAL Petr <petr.pi...@precheza.cz> > wrote: > > Hi > > > > After melt you can change levels of your factor variable. Again with the > toy example. > > > >> levels(temp$variable) > > [1] "y1

Re: [R] plotting the regression coefficients

; print(p+geom_point()) > > } > > dev.off() > > > > But the real code partly depends on your real data. > > > > Cheers > > Petr > > > > *From:* greg holly [mailto:mak.hho...@gmail.com] > *Sent:* Saturday, February 10, 2018 9:05 PM > > *

Re: [R] plotting the regression coefficients

olors-automatically-and-manually#gradient-colors-for-scatter-plots > > question. So you could find it too and probably far more quickly then > myself as I have also other duties. > > Cheers > > Petr > > BTW, you still post in HTML which could be sometimes problematic in thi

Re: [R] plotting the regression coefficients

, the plot looks very messy in one page. How can I make the plot to print out on multiple pages? Regards, Greg On Thu, Feb 8, 2018 at 4:33 PM, greg holly <mak.hho...@gmail.com> wrote: > Hi Petr; > > Thanks so much. Exactly this is what I need. I will play to change color > and so on

Re: [R] plotting the regression coefficients

r plotting it need to be reshaped > > > > library(reshape2) > > library(ggplot2) > > > > temp <- melt(temp) > > p <- ggplot(temp, aes(x=par1, y=variable, size=abs(value), > colour=factor(sign(value > > p+geom_point() > > > &

Re: [R] plotting the regression coefficients

you. > > See here for some explanation: https://www.amazon.com/Visual-Display- > Quantitative-Information/dp/0961392142/ref=sr_1_1?s=books& > ie=UTF8=1518092778=1-1=Tufte > > Bert > > > > On Feb 7, 2018 11:13 PM, "greg holly" <mak.hho...@gmail.com>

[R] Putting 733 discrete categories on Y-axis in qqplot2 as they are

Hi all; I have 733 discrete categories that will go on y-axis in ggplot2. I used the following command to put the name of x-axis. scale_x_discrete (limits = c("SI", "HOMAIR", "AIR","HOMAB","SG","DI","FI","FG")) Since there are only 8 categories on x it was easy to do. Is there any way to do the

Re: [R] Putting 733 discrete categories on Y-axis in qqplot2 as they are

b 16, 2018 at 3:39 PM, PIKAL Petr <petr.pi...@precheza.cz> wrote: > Hi > > > -Original Message- > > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of greg > holly > > Sent: Thursday, February 15, 2018 3:58 PM > > To: r-help mailing list &l

Re: [R] Putting 733 discrete categories on Y-axis in qqplot2 as they are

pecies, levels(iris$Species)[c(2,3,1)]) > > > p<-ggplot(iris, aes(x=Sepal.Length, y=Species)) > > > p+geom_point() > > > p<-ggplot(iris, aes(x=Sepal.Length, y=MySpecies)) > > > p+geom_point() > > > > > Cheers > > Petr > > > > *

Re: [R] Putting 733 discrete categories on Y-axis in qqplot2 as they are

plotting > issue is not different from factor coding. > > > > See ?read.table for details > > > > However I am not sure if it stays in original order. > > > > Cheers > > Petr > > > > *From:* greg holly [mailto:mak.hho...@gmail.com] > *Sen

[R] Error in adabag

Hi all; Happy new year. I have got the following error rror in if (nrow(object$splits) > 0) { : argument is of length zero when I am running the following codes. train <- c(sample(1:27,18), sample(28:54, 18), sample(55:81, 8)) a2011.adaboost <- boosting(median_kod ~ ., data = b[train, ],

[R] reading data problem

Hi Dear all; I have a dataset with 151*291 dimension. After making data read into R I am getting a data with 96*291 dimension. Even though I have no error message from R I could not understand the reason why I cannot get data correctly? Here are my codes to make read the data

Re: [R] reading data problem

gies for typos and terseness > > On Mon, Sep 24, 2018, 20:40 greg holly wrote: > >> Hi Jan; >> >> Thanks so much for this. Yes, I did. Her is my code to read >> data: a<-read.csv("for_R_graphs.csv", header=T, sep=",") >> >> On Mo

Re: [R] reading data problem

quot; > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Mon, Sep 24, 2018 at 11:27 AM greg holly wrote: > >> Hi Dear all; >> >> I have a dataset with 151*291 dimension. After making data read into R I >> am >> getting a d

Re: [R] reading data problem

gt; Bert Gunter > > > > > > "The trouble with having an open mind is that people keep coming along > and > > > sticking things into it." > > > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > > > > &g

Re: [R] meta analysis for sensitivity and specificity

d the note about the > mailing list). > > Best, > Wolfgang > > >-Original Message- > >From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of greg > >holly > >Sent: Thursday, 06 December, 2018 22:38 > >To: r-help mailing list > >Sub

Re: [R] meta analysis for sensitivity and specificity

d the note about the > mailing list). > > Best, > Wolfgang > > >-Original Message- > >From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of greg > >holly > >Sent: Thursday, 06 December, 2018 22:38 > >To: r-help mailing list > >Subject:

[R] meta analysis for sensitivity and specificity

Does anyone know any R library that runs meta-analysis in SAS differently for Sensitivity and Specificity if I have only the following info? Regards, Greg specificity sample_size Sensitivity Sample_size 1 21 0.66 57 1 70 0.55 33 1 19 0.76 17 1 10 0.4 30 1 16 0.46 11 [[alternative HTML

[R] label and font problems in Vennerable

Hi everyone; I am running Vennerable with 7 sets of variables. The labels are not very clear and the font size is not very visible. Does anyone know how I can change the label colors and font sizes? Regards, Greg [[alternative HTML version deleted]]

Re: [R] positive deviance plot for Binomial distribution

andard outputs when you plot a regression model. > > [1] > > https://stats.stackexchange.com/questions/322038/input-format-for-binomial-glm-in-r > > > On Fri, 25 Jan 2019, greg holly wrote: > > > Hi Dear all; > > > > I have binomially distribute

[R] differences between meat and metafor packages

Hi all; I have got different results (CI and Q value for heterogeneity, tau) on the same data when I run meta and metafor for hazard ratio with a random effects model. The basic programs for both are given below. What can cause? Regards, Greg Metafor res <- rma(HR, SE, data=a) predict(res,

Re: [R] differences between meat and metafor packages

;- rma(HR, vi=SE^2, data=a, method="REML", slab=paste(a$study), > digits=3) > > Best, > Wolfgang > > -Original Message- > From: greg holly [mailto:mak.hho...@gmail.com] > Sent: Monday, 25 February, 2019 21:20 > To: Viechtbauer, Wolfgang (SP) &g

[R] Error "sufficient values in manual scale. 10 needed but only 7 provided"

Hi Dear all; I am getting the "sufficient values in manual scale. 10 needed but only 7 provided." problem when running the followings. Your help is highly appreciated. Regards, Greg p2<-p1+scale_color_manual(name="Diseases", labels=c("Myocardial Infarction", "Coronary artery disease", "Stroke",

Re: [R] Error "sufficient values in manual scale. 10 needed but only 7 provided"

"pickup" >) >) > > class_colours <- rainbow( length( levels( mpg$classf ) ) ) > ggplot( mpg, aes( x = classf, y = cty, colour=classf ) ) + > geom_boxplot() + > scale_colour_manual( name="Class", val

[R] positive deviance plot for Binomial distribution

Hi Dear all; I have binomially distributed data (a small portion is given below) and I would like to create a distribution plot for positive deviance with "Probability of results" at Y axis and "percentage of outcome" at the x-axis. I wondered anyone knows the name of R library for this.

[R] Why I can not get work the "tidyverse" and "corrr" libraries

; I need work on libraries "tidyverse" and "corrr". When I cal these, I am getting the following error message. What can be done? Your help is highly appreciated. Greg Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

Re: [R] problem in WRS2

100 100 100 100 100 > > > > 1 1 1 1 1 1 6 > > 16.67 16.67 16.67 16.67 16.67 16.67 100.00 > > > > Maybe doing the same on your entire data set will reveal something. &g

Re: [R] problem in WRS2

code should be converting some things > to factors so p cannot be zero. Take this up with the package's maintainer. > > Bill Dunlap > TIBCO Software > wdunlap tibco.com > > > On Wed, Nov 6, 2019 at 1:58 PM greg holly wrote: > >> I got the following error message af

[R] problem in WRS2

I got the following error message after running t2way(y ~ Grup*Time, data = cp) Error in x[[grp[i]]] : attempt to select less than one element in get1index a part of the data is given below. Your help is highly appreciated. Greg > head(cp) Birey Grup Time y 1 11 Cp1

[R] Error: cannot allocate vector of size 6.5 Gb

Dear R-Help members; I have the following error messages when I would like to create training and testing data for Random Forest. Your help is highly appreciated. Regards, Greg inTrain <- createDataPartition(a, p = 0.7, list = FALSE) Error: cannot allocate vector of size 6.5 Gb

[R] write out a complete GAM fitted model equation, using parameter estimates

Hi all, I have the following results from a study. I ran this model for binary distributed outcome log(event/non_event). I need to write out a complete GAM fitted model equation, using parameter estimates given below. I have difficulty putting the parameter estimates of Spline part in the fitted

Re: [R] Sensitivity and Specificity

tor of predictions but you are > treating it as a two-dimensional matrix (presumably you think those are > the totals). > > Michael > > On 24/10/2022 16:50, greg holly wrote: > > Hi Michael, > > > > I appreciate your writing. Here are what I have after; > > >

Re: [R] Sensitivity and Specificity

return both sensitivity and specificity, along with a few other > > commonly used measures. > > > > Hope this helps, > > Jin > > > > On Tue, Oct 25, 2022 at 6:01 AM Rui Barradas > wrote: > > > >> Às 16:50 de 24/10/2022, greg holly escreveu: > &

[R] Sensitivity and Specificity

Hi all R-Help , After partitioning my data to testing and training (please see below), I need to estimate the Sensitivity and Specificity. I failed. It would be appropriate to get your help. Best regards, Greg inTrain <- createDataPartition(y=data$case, p=0.7,

Re: [R] Sensitivity and Specificity

out seeing what output you expected and what > error message you got if any but did you mean to summarise your variable > predict before doing anything with it? > > Michael > > On 24/10/2022 16:17, greg holly wrote: > > Hi all R-Help , > > > > After partitioning my

[R] sample size for beta regression

Hi all, Does anyone have experience estimating the sample size for beta regression? I have three treatment groups with 0.6, 0.5 and 0.3 mean of proportions. I tried use BetaPASS but failed, Regards, Greg [[alternative HTML version deleted]]