[R] UseDevel: version requires a more recent R
Hello R experts:
I need a developer version of a Bioconductor library.
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
When I try to useDevel it fails.
I've removed packages and again loaded but I get the same error message.
remove.packages("BiocInstaller")
source("https://bioconductor.org/biocLite.R";)
library(BiocInstaller)
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> useDevel()
Error: 'devel' version requires a more recent R
I'm running into this error for few days now. I close R after removing
biocInstaller and proceed with following steps.
Please guide me to fix this.
Thanks,
SS
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[R] How to run mixed model with related independent variables
I've data that look like: Outcome V1_AA V1_EU V1_NA V2_AA V2_EU V2_NA 0 0.046 1.001 0.954 0.045 1.001 0.954 0 0.007 1 0.993 0.007 1 0.993 1 1.774 0.217 0.009 1.774 0.217 0.009 1 0.004 1.996 0 0.004 1.996 0 1 1.001 0.997 0.002 1.001 0.997 0.002 0 0.940.998 0.061 0.940.998 0.061 0 0.587 1.407 0.006 0.587 1.408 0.006 1 0.019 1.978 0.003 0.018 1.979 0.003 Column Outcome is dependent variable. It's dichotomous either 0 or 1. Column 1st, 2nd, 3rd are three components of V1, similarly next three for V2. Sum of V1_AA, V1_EU and V1_NA will be two at each row. Similarly for V2 variable's components. Here the three predictors (I'm referring as component) are related. If AA is higher then, NA and EU will be lesser. I cannot simply use multivariate regression as: Y ~ V1_AA + V1_EU + V1_NA How do I proceed with these data? Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error while working with png output on linux server
I'm working on linux server:
Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.51-1 (2017-09-28) x86_64 GNU/Linux
I get error while creating png files. I'm sharing my commands and error while I
run those commands:
>png("abc", type="cairo")
Error in .External2(C_X11, paste0("png::", filename), g$width, g$height, :
unable to start device PNG
In addition: Warning message:
In png("abc", type = "cairo") : unable to open connection to X11 display ''
> png("apoeqqplot.png", res=600)
Error in .External2(C_X11, paste0("png::", filename), g$width, g$height, :
unable to start device PNG
In addition: Warning message:
In png("apoeqqplot.png", res = 600) :
unable to open connection to X11 display ''
dev.off()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so
LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] CMplot_3.3.1
loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2
How do I fix this?
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error while working with png output on linux server
Thanks for pointing to FAQ: I tried with cairo (shared in commands),
unfortunately didn't work.
--
Sanjeev Sariya
-Original Message-
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
Sent: Thursday, February 01, 2018 10:12 AM
To: r-help@r-project.org; Sariya, Sanjeev ;
r-help@r-project.org
Subject: Re: [R] Error while working with png output on linux server
FAQ 7.19?
Also, read the Posting Guide, in particular about posting using plain text.
--
Sent from my phone. Please excuse my brevity.
On February 1, 2018 6:50:42 AM PST, "Sariya, Sanjeev"
wrote:
>I'm working on linux server:
>Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.51-1 (2017-09-28) x86_64
>GNU/Linux
>
>I get error while creating png files. I'm sharing my commands and error
>while I run those commands:
>
>>png("abc", type="cairo")
>Error in .External2(C_X11, paste0("png::", filename), g$width,
>g$height, :
> unable to start device PNG
>In addition: Warning message:
>In png("abc", type = "cairo") : unable to open connection to X11
>display ''
>
>> png("apoeqqplot.png", res=600)
>Error in .External2(C_X11, paste0("png::", filename), g$width,
>g$height, :
> unable to start device PNG
>In addition: Warning message:
>In png("apoeqqplot.png", res = 600) :
> unable to open connection to X11 display ''
>
>dev.off()
>
>R version 3.4.2 (2017-09-28)
>Platform: x86_64-pc-linux-gnu (64-bit)
>Running under: Debian GNU/Linux 9 (stretch)
>
>Matrix products: default
>BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so
>LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so
>
>locale:
>[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>[9] LC_ADDRESS=C LC_TELEPHONE=C
>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>attached base packages:
>[1] stats graphics grDevices utils datasets methods base
>
>other attached packages:
>[1] CMplot_3.3.1
>
>loaded via a namespace (and not attached):
>[1] compiler_3.4.2 tools_3.4.2
>
>
>How do I fix this?
>
>
> [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error while working with png output on linux server
Thanks for your reply. I searched for the error on Google before resorting to
the R forum (help group).
I tried Sys.env(...) too, but didn't resolve the error I get. Hence I am
looking for solution.
--
-Original Message-
From: Thierry Onkelinx [mailto:thierry.onkel...@inbo.be]
Sent: Thursday, February 01, 2018 10:57 AM
To: Sariya, Sanjeev
Cc: Jeff Newmiller ; r-help@r-project.org
Subject: Re: [R] Error while working with png output on linux server
Dear Sanjeev,
It seems that you system neither supports X11 devices nor cairo devices. See
http://lmgtfy.com/?q=R+unable+to+open+connection+to+X11
for possible solutions.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN
BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie &
Kwaliteitszorg / Team Biometrics & Quality Assurance thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel www.inbo.be
///
To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not
data. ~ Roger Brinner The combination of some data and an aching desire for an
answer does not ensure that a reasonable answer can be extracted from a given
body of data. ~ John Tukey
///
2018-02-01 16:18 GMT+01:00 Sariya, Sanjeev :
> Thanks for pointing to FAQ: I tried with cairo (shared in commands),
> unfortunately didn't work.
>
> --
> Sanjeev Sariya
>
>
> -Original Message-
> From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
> Sent: Thursday, February 01, 2018 10:12 AM
> To: r-help@r-project.org; Sariya, Sanjeev ;
> r-help@r-project.org
> Subject: Re: [R] Error while working with png output on linux server
>
> FAQ 7.19?
>
> Also, read the Posting Guide, in particular about posting using plain text.
> --
> Sent from my phone. Please excuse my brevity.
>
> On February 1, 2018 6:50:42 AM PST, "Sariya, Sanjeev"
> wrote:
>>I'm working on linux server:
>>Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.51-1 (2017-09-28) x86_64
>>GNU/Linux
>>
>>I get error while creating png files. I'm sharing my commands and
>>error while I run those commands:
>>
>>>png("abc", type="cairo")
>>Error in .External2(C_X11, paste0("png::", filename), g$width,
>>g$height, :
>> unable to start device PNG
>>In addition: Warning message:
>>In png("abc", type = "cairo") : unable to open connection to X11
>>display ''
>>
>>> png("apoeqqplot.png", res=600)
>>Error in .External2(C_X11, paste0("png::", filename), g$width,
>>g$height, :
>> unable to start device PNG
>>In addition: Warning message:
>>In png("apoeqqplot.png", res = 600) :
>> unable to open connection to X11 display ''
>>
>>dev.off()
>>
>>R version 3.4.2 (2017-09-28)
>>Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux
>>9 (stretch)
>>
>>Matrix products: default
>>BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so
>>LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so
>>
>>locale:
>>[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>>[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>>[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>[9] LC_ADDRESS=C LC_TELEPHONE=C
>>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>>attached base packages:
>>[1] stats graphics grDevices utils datasets methods base
>>
>>other attached packages:
>>[1] CMplot_3.3.1
>>
>>loaded via a namespace (and not attached):
>>[1] compiler_3.4.2 tools_3.4.2
>>
>>
>>How do I fix this?
>>
>>
>> [[alternative HTML version deleted]]
>>
>>__
>>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide
>>http://www.R-project.org/posting-guide.html
>>and provide commented, minimal, self-contained, reproducible code.
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error while working with png output on linux server
Thank you.
--
Sanjeev Sariya
-Original Message-
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
Sent: Thursday, February 01, 2018 12:09 PM
To: Sariya, Sanjeev ; Thierry Onkelinx
Cc: r-help@r-project.org
Subject: RE: [R] Error while working with png output on linux server
This is not an R issue so this is not a good venue... it has to do with which
support software you have (not) installed. Try the R-sig-debian mailing list.
Please clarify to them how you installed R... for Debian there are relevant deb
packages and a corresponding Debian repository that provide the simplest route
to a working system, but if you compile it yourself it is easy to miss
dependencies.
--
Sent from my phone. Please excuse my brevity.
On February 1, 2018 8:23:13 AM PST, "Sariya, Sanjeev"
wrote:
>Thanks for your reply. I searched for the error on Google before
>resorting to the R forum (help group).
>I tried Sys.env(...) too, but didn't resolve the error I get. Hence I
>am looking for solution.
>
>
>
>--
>
>
>-Original Message-
>From: Thierry Onkelinx [mailto:thierry.onkel...@inbo.be]
>Sent: Thursday, February 01, 2018 10:57 AM
>To: Sariya, Sanjeev
>Cc: Jeff Newmiller ; r-help@r-project.org
>Subject: Re: [R] Error while working with png output on linux server
>
>Dear Sanjeev,
>
>It seems that you system neither supports X11 devices nor cairo
>devices. See http://lmgtfy.com/?q=R+unable+to+open+connection+to+X11
>for possible solutions.
>
>Best regards,
>
>ir. Thierry Onkelinx
>Statisticus / Statistician
>
>Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN
>BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie
>& Kwaliteitszorg / Team Biometrics & Quality Assurance
>thierry.onkel...@inbo.be Havenlaan 88 bus 73, 1000 Brussel www.inbo.be
>
>///
> To call in the statistician after the experiment
>is done may be no more than asking him to perform a post-mortem
>examination: he may be able to say what the experiment died of. ~ Sir
>Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger
>Brinner The combination of some data and an aching desire for an answer
>does not ensure that a reasonable answer can be extracted from a given
>body of data. ~ John Tukey
>///
>
>
>
>
>
>2018-02-01 16:18 GMT+01:00 Sariya, Sanjeev :
>> Thanks for pointing to FAQ: I tried with cairo (shared in commands),
>unfortunately didn't work.
>>
>> --
>> Sanjeev Sariya
>>
>>
>> -Original Message-
>> From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
>> Sent: Thursday, February 01, 2018 10:12 AM
>> To: r-help@r-project.org; Sariya, Sanjeev ;
>
>> r-help@r-project.org
>> Subject: Re: [R] Error while working with png output on linux server
>>
>> FAQ 7.19?
>>
>> Also, read the Posting Guide, in particular about posting using plain
>text.
>> --
>> Sent from my phone. Please excuse my brevity.
>>
>> On February 1, 2018 6:50:42 AM PST, "Sariya, Sanjeev"
> wrote:
>>>I'm working on linux server:
>>>Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.51-1 (2017-09-28) x86_64
>>>GNU/Linux
>>>
>>>I get error while creating png files. I'm sharing my commands and
>>>error while I run those commands:
>>>
>>>>png("abc", type="cairo")
>>>Error in .External2(C_X11, paste0("png::", filename), g$width,
>>>g$height, :
>>> unable to start device PNG
>>>In addition: Warning message:
>>>In png("abc", type = "cairo") : unable to open connection to X11
>>>display ''
>>>
>>>> png("apoeqqplot.png", res=600)
>>>Error in .External2(C_X11, paste0("png::", filename), g$width,
>>>g$height, :
>>> unable to start device PNG
>>>In addition: Warning message:
>>>In png("apoeqqplot.png", res = 600) :
>>> unable to open connection to X11 display ''
>>>
>>>dev.off()
>>>
>>>R version 3.4.2 (2017-09-28)
>>>Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian
>GNU/Linux
>>>9 (stretch)
>>>
>>>Matrix products: default
>>>BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so
>>>LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so
>>>
>>>locale:
>>>[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>&
Re: [R] change location of temporary files
You can set this in script as:
library("unixtools ")
set.tempdir("/home/path_to_dir/temp_dir/")
--
Sanjeev
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Kumar Mainali
Sent: Friday, February 23, 2018 1:53 PM
To: R Help
Subject: [R] change location of temporary files
I would like to change where R stores the temporary files to my external hard
drive in my iMac. This is important because the temporary files R creates are
huge and I do not have enough available space in my internal HD. Again, this is
for macOS.
This change has to be temporary. Later I need to use the usual location for
temp files in the internal HD.
Thanks in advance,
Kumar Mainali
--
Postdoctoral Associate
Department of Biology
University of Maryland, College Park
ᐧ
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Help with apply and new column?
Hello members, Can I ask question for apply, adding new column to data frame on this e-mail list? Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with apply and new column?
Thanks. I think nabble is good for programming questions. Bear with me if I'm
incorrect.
Data: Genomics SNP information
Goal: I need to add Chromosome and SNP position to the data frame I'm using
through apply.
I'd like to add new column from text processed through apply function.
For example: 10:60523:T:G (Column 2)
CHR: 10
Position: 60523
Dataset:
chr rs ps n_miss allele1 allele0 af betase l_remle
p_wald
-9 10:60523:T:G-9 0 T G 0.977 -1.769354e-02
3.597196e-021.566731e-016.228309e-01
-9 10:60684:A:C-9 0 A C 0.973 1.698925e-02
2.942366e-021.561001e-015.636926e-01
-9 10:61331:A:G-9 0 A G 0.973 1.708586e-02
2.942424e-021.560944e-015.614851e-01
-9 10:62010:C:T-9 0 C T 0.980 -8.513143e-03
3.837054e-021.566875e-018.244260e-01
Code:
data<-read.table("small.txt",header = T) # read data
data<-data[,c(2,11)] #delete other columns not needed
#--split data on : and get chromosome and position
split_rs<-function(rs){
chr<-vector(,length(rs)) # create new vector to store chr
pos<-vector(,length(rs)) #create new vector to store position
for(i in 1:length(rs)){ #iterate over RS column
if(grepl(":",rs[i])){ #if : in column string
temp <- strsplit(rs[i],":",fixed=T) #split
chr[i] <-temp[[1]][1] #store CHR
pos[i] <- temp[[1]][2] #store position
}
}
return(list(chr=chr,pos=pos)) #return making a list
}
data$POS<-"NA" #add new column CHR and make NA
data$CHR <- "NA" #add new column POS and make NA
temp<-apply(data,2,split_rs) #send data frame to function
#--I assign value from list sent -- I would like to improve this part
data$CHR<-temp$rs$chr
data$POS<-temp$rs$pos
rm(temp)
colnames(data)<-c("SNP","P","CHR","BP")
-Original Message-
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
Sent: Monday, March 5, 2018 1:48 PM
To: r-help@r-project.org; Sariya, Sanjeev ; R Help
Subject: Re: [R] Help with apply and new column?
Read the Posting Guide... (see message footer) ... some relevant things you can
find there:
a) Yes, this appears to be about how to use an R base function so it is on topic
b) Post a reproducible example (include some sample data, preferably using the
dput function)
c) Post using plain text so the mailing list doesn't convert it for you and
mangle things in a way you did not intend.
--
Sent from my phone. Please excuse my brevity.
On March 5, 2018 10:07:24 AM PST, "Sariya, Sanjeev"
wrote:
>Hello members,
>
>Can I ask question for apply, adding new column to data frame on this
>e-mail list?
>
>Thanks!
>
>
>
> [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with apply and new column?
Thank you, that helps.
-Original Message-
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
Sent: Monday, March 5, 2018 3:36 PM
To: Sariya, Sanjeev
Cc: r-help@r-project.org; R Help
Subject: RE: [R] Help with apply and new column?
Comments interspersed, and some code at the end.
On Mon, 5 Mar 2018, Sariya, Sanjeev wrote:
> Thanks. I think nabble is good for programming questions. Bear with me
> if I'm incorrect.
You may have found R-help archives at Nabble, but R-help has nothing to do with
Nabble.
>
> Data: Genomics SNP information
I know almost nothing about using R for genomics.
> Goal: I need to add Chromosome and SNP position to the data frame I'm using
> through apply.
>
> I'd like to add new column from text processed through apply function.
>
> For example: 10:60523:T:G (Column 2)
> CHR: 10
> Position: 60523
Assuming Position is "P", what are your "SNP" and "BP" in the names you
assigned below as c("SNP","P","CHR","BP")?
> Dataset:
> chr rs ps n_miss allele1 allele0 af betase l_remle
> p_wald
> -910:60523:T:G-9 0 T G 0.977 -1.769354e-02
> 3.597196e-021.566731e-016.228309e-01
> -910:60684:A:C-9 0 A C 0.973 1.698925e-02
> 2.942366e-021.561001e-015.636926e-01
> -910:61331:A:G-9 0 A G 0.973 1.708586e-02
> 2.942424e-021.560944e-015.614851e-01
> -910:62010:C:T-9 0 C T 0.980 -8.513143e-03
> 3.837054e-021.566875e-018.244260e-01
>
> Code:
>
>
> data<-read.table("small.txt",header = T) # read data
> data<-data[,c(2,11)] #delete other columns not needed
>
> #--split data on : and get chromosome and position
>
> split_rs<-function(rs){
>
>chr<-vector(,length(rs)) # create new vector to store chr
>pos<-vector(,length(rs)) #create new vector to store position
>
>for(i in 1:length(rs)){ #iterate over RS column
>
>if(grepl(":",rs[i])){ #if : in column string
>temp <- strsplit(rs[i],":",fixed=T) #split
>chr[i] <-temp[[1]][1] #store CHR
>pos[i] <- temp[[1]][2] #store position
>}
>}
>return(list(chr=chr,pos=pos)) #return making a list }
>
> data$POS<-"NA" #add new column CHR and make NA data$CHR <- "NA" #add
> new column POS and make NA
>
> temp<-apply(data,2,split_rs) #send data frame to function
>
> #--I assign value from list sent -- I would like to improve this part
>
> data$CHR<-temp$rs$chr
> data$POS<-temp$rs$pos
>
> rm(temp)
>
> colnames(data)<-c("SNP","P","CHR","BP")
>
##
# Your code was pretty severely broken... it would not run, # and I don't know
what you expected to see as output.
# 1) data is the name of a function in base R... re-using
#it can lead to puzzling errors
# 2) With all this character manipulation, you need to read
#your character data in as character, not as factors
# 3) Don't use the T variable... use the constant TRUE,
#since T can easily be overwritten to some non-TRUE value.
dta <- read.table( "small.txt", header = TRUE, as.is = TRUE ) # read data dta
<- dta[ , c( 2, 11 ) ] #delete other columns not needed
# 4) Not at all clear why you want to split all of the columns
#using apply( ..., 2, ... ) when only one column has ":" characters
#temp <- apply( dta, 2, split_rs ) #send data frame to function temp <-
strsplit( dta$rs, ":" ) # gets the whole column splits at once
# wildly guessing here
rs_chrmatrix <- do.call( rbind, temp )
rs_DF <- as.data.frame( rs_chrmatrix, stringsAsFactors = FALSE ) names( rs_DF )
<- c( "CHR", "P", "X1", "X2" ) rs_DF$P <- as.integer( rs_DF$P )
str( rs_DF )
##
>
> -Original Message-
> From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
> Sent: Monday, March 5, 2018 1:48 PM
> To: r-help@r-project.org; Sariya, Sanjeev ;
> R Help
> Subject: Re: [R] Help with apply and new column?
>
> Read the Posting Guide... (see message footer) ... some relevant things you
> can find there:
>
> a) Yes, this appears to be about how to use an R base function so it
> is on topic
> b) Post a reproducible example (include some sample data, preferably
> using the dput funct
Re: [R] Hacked
I've been receiving nasty e-mails too. No g-mail, but official/work e-mail address. -Original Message- From: R-help On Behalf Of Rui Barradas Sent: Tuesday, April 17, 2018 5:09 PM To: Ding, Yuan Chun ; Fowler, Mark ; Luis Puerto ; Peter Langfelder Cc: R-Help ML R-Project ; Neotropical bat risk assessments Subject: Re: [R] Hacked Hello, Nor do I, no gmail, also got spam. Rui Barradas On 4/17/2018 8:34 PM, Ding, Yuan Chun wrote: > No, I do not use gmail, still got dirty spam email twice. > > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of > Fowler, Mark > Sent: Tuesday, April 17, 2018 12:32 PM > To: Luis Puerto; Peter Langfelder > Cc: R-Help ML R-Project; Neotropical bat risk assessments > Subject: Re: [R] Hacked > > [Attention: This email came from an external source. Do not open > attachments or click on links from unknown senders or unexpected > emails.] > > > > > > Just an observation. I have not seen the spam you are discussing. Possibly it > is specific to gmail addresses? > > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Luis > Puerto > Sent: April 17, 2018 4:11 PM > To: Peter Langfelder > Cc: R-Help ML R-Project; Neotropical bat risk assessments > Subject: Re: [R] Hacked > > Hi! > > This happened to me also! I just got a spam email just after posting and then > in following days I got obnoxious spam emails in my spam filter. As the > others, I think that there is some kind of bot subscribed to the list, but > also perhaps a spider or crawler monitoring the R-Help archive and getting > email addresses there. Nabble is a possibility too. > >> On 17 Apr 2018, at 21:50, Peter Langfelder >> wrote: >> >> I got some spam emails after my last post to the list, and the emails >> did not seem to go through r-help. The spammers may be subscribed to >> the r-help, or they get the poster emails from some of the web copies >> of this list (nabble or similar). >> >> Peter >> >> On Tue, Apr 17, 2018 at 11:37 AM, Ulrik Stervbo >> wrote: >>> I asked the moderators about it. This is the reply >>> >>> "Other moderators have looked into this a bit and may be able to >>> shed more light on it. This is a "new" tactic where the spammers >>> appear to reply to the r-help post. They are not, however, going through >>> the r-help server. >>> >>> It also seems that this does not happen to everyone. >>> >>> I am not sure how you can automatically block the spammers. >>> >>> Sorry I cannot be of more help." >>> >>> --Ulrik >>> >>> Jeff Newmiller schrieb am Di., 17. Apr. >>> 2018, >>> 14:59: >>> Likely a spammer has joined the mailing list and is auto-replying to posts made to the list. Unlikely that the list itself has been "hacked". Agree that it is obnoxious. On April 17, 2018 5:01:10 AM PDT, Neotropical bat risk assessments < neotropical.b...@gmail.com> wrote: > Hi all, > > Site has been hacked? > Bad SPAM arriving > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Sent from my phone. Please excuse my brevity. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. >>> >>> [[alternative HTML version deleted]] >>> >>> __ >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >> >> __ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do r
Re: [R] Something simple not working in group_by
Strange. Worked fine on: R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 9 (stretch) Commands: m <- data.frame( id = rep(1:3, each=2), score = rep(c(6,3), each=3) ) as.data.frame(m %>% group_by(id) %>% mutate(total = cumsum(score))) id score total 1 1 6 6 2 1 612 3 2 6 6 4 2 3 9 5 3 3 3 6 3 3 6 -Original Message- From: R-help On Behalf Of Sumitrajit Dhar Sent: Monday, July 9, 2018 5:35 PM To: r-help@r-project.org Subject: [R] Something simple not working in group_by Hi Folks, I am trying to get a group_by cumsum using: R version 3.5.0 (2018-04-23) -- "Joy in Playing" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit) Here is an example of a simple construct that is not working. m <- data.frame( id = rep(1:3, each=2), score = rep(c(6,3), each=3) ) m %>% group_by(id) %>% mutate(total = cumsum(score)) My output: # A tibble: 6 x 3 # Groups: id [3] id score total 1 1 6 6 2 1 612 3 2 618 4 2 321 5 3 324 6 3 327 What am I missing? Thanks in advance. Regards, Sumit __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
