Re: [R] Error in is biallelic

2020-11-06 Thread John Kane
Ah, good point. On Fri, 6 Nov 2020 at 20:24, David Winsemius wrote: > > On 11/6/20 4:11 PM, John Kane wrote: > > I think we need a lot mole information. > > > > see these links for suggestions on how to ask a question. > > > > http://adv-r.had.co.nz/Reproducibility.html > > > > >

Re: [R] Error in is biallelic

2020-11-06 Thread David Winsemius
On 11/6/20 4:11 PM, John Kane wrote: I think we need a lot mole information. see these links for suggestions on how to ask a question. http://adv-r.had.co.nz/Reproducibility.html http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example I agree that more

Re: [R] Error in is biallelic

2020-11-06 Thread John Kane
I think we need a lot mole information. see these links for suggestions on how to ask a question. http://adv-r.had.co.nz/Reproducibility.html http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example On Fri, 6 Nov 2020 at 14:37, Sakthipriya M wrote: > Hi, > am

Re: [R] how to order variables on correlation plot

2020-11-06 Thread Ana Marija
Thank you! On Fri, Nov 6, 2020 at 1:45 PM David Winsemius wrote: > > Why did you specify a different order parameter if that is not what you > wanted? > > Suggest you look more carefully at the parameters of the code you are copying > and pasting and also at the help page, ?corrplot . > > -- >

Re: [R] how to order variables on correlation plot

2020-11-06 Thread David Winsemius
Why did you specify a different order parameter if that is not what you wanted? Suggest you look more carefully at the parameters of the code you are copying and pasting and also at the help page, ?corrplot . -- David. On 11/6/20 6:08 AM, Ana Marija wrote: > sorry forgot to attach the plot.

[R] Error in is biallelic

2020-11-06 Thread Sakthipriya M
Hi, am trying to run the following using my SNP data vcf file maizelight <- vcfR2genlight(maizevcf,n.cores=1) Why am getting error Error in is.biallelic(x) : trying to get slot "fix" from an object (class "spec_tbl_df") that is not an S4 object anybody help to solve this, am just trying

Re: [R] Bootstrap P-Value

2020-11-06 Thread AbouEl-Makarim Aboueissa
Dear Greg: H0: Mean 1- Mean 2 = 0 Ha: Mean 1 - Mean 2 ! = 0 with many thanks abou __ *AbouEl-Makarim Aboueissa, PhD* *Professor, Statistics and Data Science* *Graduate Coordinator* *Department of Mathematics and Statistics* *University of Southern Maine* On Fri, Nov 6,

Re: [R] Bootstrap P-Value

2020-11-06 Thread Greg Snow
A p-value is for testing a specific null hypothesis, but you do not state your null hypothesis anywhere. It is the null value that needs to be subtracted from the bootstrap differences, not the observed difference. By subtracting the observed difference you are setting a situation where the

Re: [R] [External] Re: how to order variables on correlation plot

2020-11-06 Thread Richard M. Heiberger
My guess is that the "%>% data.frame %>%" step turned something into a character that you thought would be a factor. See this example. Remember that the stringsAFactors argument to data.frame was recently changed. > tmp <- data.frame(A=c("A","F","B","G","C"), B=1:5, CC=6:10) > tmp A B CC 1 A

[R] Bootstrap P-Value

2020-11-06 Thread AbouEl-Makarim Aboueissa
*Dear All:* *I am trying to compute the p-value of the bootstrap test; please see below.* *In example 1 the p-value agrees with the confidence interval.* *BUT, in example 2 the p-value DOES NOT agree with the confidence interval. In Example 2, the p-value should be zero or close to zero.* *I

Re: [R] how to order variables on correlation plot

2020-11-06 Thread Ana Marija
sorry forgot to attach the plot. On Fri, Nov 6, 2020 at 8:07 AM Ana Marija wrote: > > Hello > > I have data like this: > > > head(my_data) > subjects DIABDUR HBA1C ESRD SEX AGE PHENO C1 C2 > 1 fam0110_G110 38 9.41 2 51 2 -0.01144980 0.002661140 > 2

[R] how to order variables on correlation plot

2020-11-06 Thread Ana Marija
Hello I have data like this: > head(my_data) subjects DIABDUR HBA1C ESRD SEX AGE PHENO C1 C2 1 fam0110_G110 38 9.41 2 51 2 -0.01144980 0.002661140 2 fam0113_G113 30 12.51 2 40 2 -0.00502052 -0.000929061 3 fam0114_G114 23 8.4

Re: [R] backslash in xtable (generate latex code from R)

2020-11-06 Thread Marc Schwartz via R-help
Hi, It looks like xtable is "sanitizing" special characters in the LaTeX output by default, by adding a double backslash, so that LaTeX will process the characters as literals, rather than specials. It is not parsing the boundary '$' characters to define insertion of math symbols inside text

Re: [R] backslash in xtable (generate latex code from R)

2020-11-06 Thread Thierry Onkelinx via R-help
You could use kable() from the knitr package. kable(mytable, format = "latex", escape = FALSE) \begin{tabular}{l} \hline $\beta_0$\\ \hline aa\\ \hline bb\\ \hline cc$\alpha_1$\\ \hline \end{tabular} ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders

[R] backslash in xtable (generate latex code from R)

2020-11-06 Thread John
I'd like to have $\alpha_1$ in my table, and the column name is $\beta_0$ library(xtable) mytable <- data.frame(beta_0 = c("aa","bb","cc$\\alpha_1$")) colnames(mytable) <- "$\\beta_0$" print(xtable(mytable), include.rownames = F, sanitize.colnames.function = identity) No problem with