[R] Adding markers and text for some data points after drawing a plot

Hi All, I have a data set of around 17,000 gene names and their lengths. E.g.   gene  kblength     A3GALT2   14.333    AADACL3   12.609    AADACL4   22.532         ABCA4 128.312        ABCB10  42.114      ABCD3    100.287 . and

Re: [R] Adding markers and text for some data points after drawing a plot

26, 2013 1:54 PM Subject: Re: [R] Adding markers and text for some data points after drawing a plot On Feb 26, 2013, at 1:04 PM, Debs Majumdar wrote: Hi All, I have a data set of around 17,000 gene names and their lengths. E.g.           gene      kblength      A3GALT2      14.333

Re: [R] Order variables automatically

Sorry for not being clear.  I forgot to mention that the variable labels don't really say which are categorical/continuous. They are just I1, I2,, I459. Out of these 459 variables, most are continuous and others are categorical. So, the grep command won't work here. Thanks, Debs

Re: [R] Order variables automatically

not ordered factors, instead of grep the following might work. vars.to.order - sapply(yourdata, is.factor) And the rest should be the same. Hope this helps, Rui Barradas Em 01-01-2013 10:13, Debs Majumdar escreveu: Sorry for not being clear.  I forgot to mention that the variable labels

Re: [R] Order variables automatically

are categorical. If they are factors, just not ordered factors, instead of grep the following might work. vars.to.order - sapply(yourdata, is.factor) And the rest should be the same. Hope this helps, Rui Barradas Em 01-01-2013 10:13, Debs Majumdar escreveu: Sorry for not being clear.  I forgot

[R] Order variables automatically

Hi, I have a dataset with 6 categorical variables. I have used this following code to make the variables u1-u6 ordered factors and this works well. cat1cat2 cat3 cat4 cat5 cat6   0      1     1  0     0     1   1      1     0      0     0     0 ...

Re: [R] Storing results in a single file after looping over all files

have 750 unique IDs in each of the raw datasets. Thanks, Debs From: Jean V Adams jvad...@usgs.gov To: Debs Majumdar debs_st...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Thursday, June 28, 2012 12:05 PM Subject: Re: [R] Storing results in a single

[R] Storing results in a single file after looping over all files

Hi All, I have a whole lot of *.raw files in my working folder and I am doing the same analysis on each of those and want to save all the results in a single file. I am making some mistake here and can't figure out how to solve it. Say, the *.raw files are ABCD.raw, EFGH.raw, IJKL.raw ...

[R] weird --no 'dimnames' attribute for array-- error for R lordif package

Hi All,   I am trying to use the lordif package in R and can't figure out the reason for the above error when I try to run the calctheta() function. ## # read data using foreign package - must be Stata 11 or earlier racedata- read.dta(race.dta)    # item responses

[R] Save multiple plots in a single pdf file when the plots are generated by a single plot command

Hi, I am trying to save multiple plots in a single pdf file when  the plots are generated by a single plot command. I am using the lordif package which generates multiple plots with one command. pdf(education.pdf) plot.lordif(ed_dif, labels = c(White, African American)) dev.off() And this is

Re: [R] Save multiple plots in a single pdf file when the plots are generated by a single plot command

  2   - Original Message - From: R. Michael Weylandt michael.weyla...@gmail.com To: Debs Majumdar debs_st...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Friday, June 15, 2012 3:48 PM Subject: Re: [R] Save multiple plots in a single pdf file when

Re: [R] Save multiple plots in a single pdf file when the plots are generated by a single plot command

I thought that might be the case and did a couple of dev.off() even though I started a new R session. Each time I try to use the plot, it comes up with pdf 2. - Original Message - From: R. Michael Weylandt michael.weyla...@gmail.com To: Debs Majumdar debs_st...@yahoo.com Cc: r-help@r

[R] hexplom question(s)

Hi,    I am trying to use the --hexplom-- function to draw a scatterplot matrix. The following works for me: hexplom(~file[,1:4], xbins=15,  xlab=) However, I want to make some changes to the graph: a) I only want to print/draw only one-half of the plot. Is there anyway to get rid of the

[R] What package is used for the following graph?

Hi All,   I am trying to figure out what package was used to create the following graph? http://f.imgtmp.com/MZjwy.png Thanks,   Debs __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

[R] Looping over files

Hi,  I have a list of files in one of my working directories: chr17.chunk1.dose.fvd chr17.chunk1.dose.fvi chr17.chunk1.prob.fvd  chr17.chunk1.prob.fvi  ... . chr17.chunk10.dose.fvd chr17.chunk10.dose.fvi chr17.chunk10.prob.fvd chr17.chunk10.prob.fvi And I

[R] (no subject)

http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] gsub help

Hi,  I am working with the following list of files: [1] study_chr1.one.phased.impute2.chunk1   [2] study_chr1.one.phased.impute2.chunk1_info  [3] study_chr1.one.phased.impute2.chunk1_info_by_sample [4] study_chr1.one.phased.impute2.chunk1_summary   [5]

Re: [R] Reading in and modifying multiple datasets in a loop

=TRUE, old=FALSE) } # Thanks,  Debs - Original Message - From: Debs Majumdar debs_st...@yahoo.com To: r-help@r-project.org r-help@r-project.org Cc: Sent: Friday, October 21, 2011 2:32 PM Subject: Reading in and modifying multiple datasets in a loop Hi,   I have been given a set

[R] Reading in and modifying multiple datasets in a loop

Hi,   I have been given a set of around 300 files where there are 5 files corresponding to each chunk. E.g. Chunk 1 for chr1 contains these 5 files:         chr1.one.phased.impute2.chunk1     chr1.one.phased.impute2.chunk1_info     chr1.one.phased.impute2.chunk1_info_by_sample    

[R] Error in evalauating a function

Hi,   I am very new to R. So, pardon my dumb question. I was trying to write my own function to run a different model (perform an ordered logistic regression) using the example in website http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml But R returns a error `R Error in eval(expr,

Re: [R] Error in evalauating a function

variable (PHENO) and the covariate (COVAR) is contained in the file p3.txt. I added the option --R-debug to get the output below.  Thanks,  Debs - Original Message - From: Debs Majumdar debs_st...@yahoo.com To: r-help@r-project.org r-help@r-project.org Cc: Sent: Tuesday, August 30, 2011 3

[R] Ordinal logistic regression p-values

Hi,    Are there any packages which prints out p-values for OLR's (like `ologit' from Stata)? I want to run a bunch of OLRs and print the p-value for the first coefficient from each of them.   I checked polr() under MASS and it doesn't.  There's a lrm() function under Design which does print

[R] Dealing with missing values in a linear mixed model

Hello,    I am trying to run a linear mixed model using model.a - lme(Psstotals ~ Visit, data=caf, random= ~ Visit|Id) My dataset looks lie the following:     Id   Visit  Agecorrected Psstotals 1 106 0   19    8 2 106 1   19    9     3

[R] Speed up an R code

Hello,   Are there some basic things one can do to speed up a R code? I am new to R and currently going through the following situation.   I have run a R code on two different machines. I have R 2.12 installed on both.   Desktop 1 is slightly older and has a dual core processor with 4gigs of

[R] superimposing some random points on a plot

Hi All, i) I wanted a plot with a x axis that ranges from 25 to 75 points  and 2 normal curves on it with y-axis suppressed. ii) One with mean 60 and standard error 2 and the other one with mean 40 and standard error 5. iii) At last, I'd like you to pull some random values from those