I have 682 variables in a data frame , and a function that I should feed 682 variables in this function one by one and each time save the file as a special name! for emaple: my data frame file includes 682 names : 1 aaa 2 bbb 3 dfdsfg 4 fghh . 682 fgfhg and a function like prep(Z, aaa, .....) and each time I should change the variable name in this function and read the variable from the data frame and each time I should save the file as a special name such as: prep1<- prep(z, aaa,...) prep2<- prep(z, bbb,...) prep3<- prep(z, dfdsfg,..) Prep4<- prep(z, fghh,...) How can I use loop function in R to that? Thanks [[alternative HTML version deleted]]
for (var_name in names(z)) {
# assuming the prep function writes the content of z$var_name to the file
var_name.csv
prep(z, var_name)
}
On Wed, Jul 1, 2015 at 10:18 PM Lida Zeighami <lid.zigh at gmail.com>
wrote:
> I have 682 variables in a data frame , and a function that I should feed
> 682 variables in this function one by one and each time save the file as a
> special name!
> for emaple:
> my data frame file includes 682 names :
> 1 aaa
> 2 bbb
> 3 dfdsfg
> 4 fghh
> .
>
> 682 fgfhg
> and a function like prep(Z, aaa, .....) and each time I should change the
> variable name in this function and read the variable from the data frame
> and each time I should save the file as a special name such as:
>
> prep1<- prep(z, aaa,...)
> prep2<- prep(z, bbb,...)
> prep3<- prep(z, dfdsfg,..)
> Prep4<- prep(z, fghh,...)
>
> How can I use loop function in R to that?
>
> Thanks
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
You never said how you wanted to save the data, so I will choose to use
'saveRDS' which should handle most anything.
for (i in name_file$names){
saveRDS(prep(z, i), file = paste0(i, '.RDS'))
}
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.
On Wed, Jul 1, 2015 at 2:07 PM, Lida Zeighami <lid.zigh at gmail.com>
wrote:
> I have 682 variables in a data frame , and a function that I should feed
> 682 variables in this function one by one and each time save the file as a
> special name!
> for emaple:
> my data frame file includes 682 names :
> 1 aaa
> 2 bbb
> 3 dfdsfg
> 4 fghh
> .
>
> 682 fgfhg
> and a function like prep(Z, aaa, .....) and each time I should change the
> variable name in this function and read the variable from the data frame
> and each time I should save the file as a special name such as:
>
> prep1<- prep(z, aaa,...)
> prep2<- prep(z, bbb,...)
> prep3<- prep(z, dfdsfg,..)
> Prep4<- prep(z, fghh,...)
>
> How can I use loop function in R to that?
>
> Thanks
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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]]
I forgot that you also wanted to change the variable name; I would suggest
that you don't use individual objects, but instead use a 'list'.
Here is
how it would change
result <- lapply(name_file$names, function(.file){
result <- prep(z, .file)
saveRDS(result, file = paste0(.file, '.RDS'))
result # return value that goes in the list
})
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.
On Wed, Jul 1, 2015 at 9:00 PM, jim holtman <jholtman at gmail.com> wrote:
> You never said how you wanted to save the data, so I will choose to use
> 'saveRDS' which should handle most anything.
>
> for (i in name_file$names){
> saveRDS(prep(z, i), file = paste0(i, '.RDS'))
> }
>
>
>
> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
> Tell me what you want to do, not how you want to do it.
>
> On Wed, Jul 1, 2015 at 2:07 PM, Lida Zeighami <lid.zigh at gmail.com>
wrote:
>
>> I have 682 variables in a data frame , and a function that I should
feed
>> 682 variables in this function one by one and each time save the file
as a
>> special name!
>> for emaple:
>> my data frame file includes 682 names :
>> 1 aaa
>> 2 bbb
>> 3 dfdsfg
>> 4 fghh
>> .
>>
>> 682 fgfhg
>> and a function like prep(Z, aaa, .....) and each time I should change
the
>> variable name in this function and read the variable from the data
frame
>> and each time I should save the file as a special name such as:
>>
>> prep1<- prep(z, aaa,...)
>> prep2<- prep(z, bbb,...)
>> prep3<- prep(z, dfdsfg,..)
>> Prep4<- prep(z, fghh,...)
>>
>> How can I use loop function in R to that?
>>
>> Thanks
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at 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]]
Thank you so much for replying me! for better understanding my problem, I explain my problem more: I have a 682*1 matrix called "met" , the first 5 rows similar below:> rownames(met)[1:5][1] "glycine_imp" [2] "Nacetylglycine_imp" [3] "sarcosine_imp" [4] "dimethylglycine_imp" [5] "betaine_imp" and I have a function in R that each time use one of the row names of "met" matrix and create a new object file and I should save the objects! my function is " Scores(Z=metalofGT,formula="met[i]~egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+GENDER") " that each time just I should change the met[i] and replace by row names "met" one by one and for each of them I should rename the function and after that I should save each object! for example for first row of "met" I have> prep1<- Scores(Z=metalofGT,formula="glycine_imp~egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+GENDER")#creat the object file for first row and called prep1###> save(prep1, file="prep1.RData", compress="bzip2") ##save theobject file as "prep1.RData"##### I should do this process for 682 row names of "met" matrix and at the end I should have "prep1.RData" , "prep2.RData" , "prep3.RData" so, would you please help me how to do it? Many Thanks, Ati On Wed, Jul 1, 2015 at 1:07 PM, Lida Zeighami <lid.zigh at gmail.com> wrote:> I have 682 variables in a data frame , and a function that I should feed > 682 variables in this function one by one and each time save the file as a > special name! > for emaple: > my data frame file includes 682 names : > 1 aaa > 2 bbb > 3 dfdsfg > 4 fghh > . > > 682 fgfhg > and a function like prep(Z, aaa, .....) and each time I should change the > variable name in this function and read the variable from the data frame > and each time I should save the file as a special name such as: > > prep1<- prep(z, aaa,...) > prep2<- prep(z, bbb,...) > prep3<- prep(z, dfdsfg,..) > Prep4<- prep(z, fghh,...) > > How can I use loop function in R to that? > > Thanks >[[alternative HTML version deleted]]
Hi
I cannot test it in absence of data. Anyway I would not use saving single
objects but use list instead.
Something like
lll <- vector(mode="list", nrow(met))
for (i in 1:nrow(met)) {
form <- as.formula(paste(met[i], "~
egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+GENDER"))
lll[i] <- Scores(Z=metalofGT,formula=form)
}
Cheers
Petr
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Lida
> Zeighami
> Sent: Thursday, July 02, 2015 6:48 PM
> To: r-help at r-project.org
> Subject: Re: [R] question
>
> Thank you so much for replying me!
> for better understanding my problem, I explain my problem more:
>
> I have a 682*1 matrix called "met" , the first 5 rows similar
below:
>
> > rownames(met)[1:5]
>
> [1] "glycine_imp"
> [2] "Nacetylglycine_imp"
> [3] "sarcosine_imp"
> [4] "dimethylglycine_imp"
> [5] "betaine_imp"
>
> and I have a function in R that each time use one of the row names of
> "met"
> matrix and create a new object file and I should save the objects!
>
> my function is "
>
Scores(Z=metalofGT,formula="met[i]~egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+G
> ENDER")
> " that each time just I should change the met[i] and replace by row
> names
> "met" one by one and for each of them I should rename the
function and
> after that I should save each object!
> for example for first row of "met" I have
>
> > prep1<-
>
Scores(Z=metalofGT,formula="glycine_imp~egfr_v1_ckdepi+pc1+pc2+pc3+V1AG
> E01+GENDER")
> #creat the object file for first row and called prep1###
>
> > save(prep1, file="prep1.RData",
compress="bzip2") ##save the
> object file as "prep1.RData"#####
>
> I should do this process for 682 row names of "met" matrix and at
the
> end I
> should have "prep1.RData" , "prep2.RData" ,
"prep3.RData"
>
> so, would you please help me how to do it?
>
> Many Thanks,
> Ati
>
> On Wed, Jul 1, 2015 at 1:07 PM, Lida Zeighami <lid.zigh at gmail.com>
> wrote:
>
> > I have 682 variables in a data frame , and a function that I should
> feed
> > 682 variables in this function one by one and each time save the file
> as a
> > special name!
> > for emaple:
> > my data frame file includes 682 names :
> > 1 aaa
> > 2 bbb
> > 3 dfdsfg
> > 4 fghh
> > .
> >
> > 682 fgfhg
> > and a function like prep(Z, aaa, .....) and each time I should change
> the
> > variable name in this function and read the variable from the data
> frame
> > and each time I should save the file as a special name such as:
> >
> > prep1<- prep(z, aaa,...)
> > prep2<- prep(z, bbb,...)
> > prep3<- prep(z, dfdsfg,..)
> > Prep4<- prep(z, fghh,...)
> >
> > How can I use loop function in R to that?
> >
> > Thanks
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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.
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Hi Ati,
Let's start from the top and see where we finish up. I'll use a
somewhat smaller matrix:
met<-matrix(runif(5),ncol=1)
rownames(met)<-c("glycine_imp","Nacetylglycine_imp","sarcosine_imp",
"dimethylglycine_imp","betaine_imp")
met
[,1]
glycine_imp 0.61532855
Nacetylglycine_imp 0.04294675
sarcosine_imp 0.98840385
dimethylglycine_imp 0.00507230
betaine_imp 0.68528107
In your example, I think you are mixing up the names and the values of
"met". I suspect that you want to use the values for the computation
and the names for the filenames. Also, a one column matrix will act
very much like a vector, but there are a few problems if you treat it
like one. For instance, if you extract a value as though met is a
vector:
met[2]
[1] 0.04294675
you just get the value, not the rowname. Using both indices extracts
both the value and the name.
met[2,1]
Nacetylglycine_imp
0.04294675
As I don't have any idea what the other values in your formula are, I
will take the liberty of giving them some:
metalofGT<-100
egfr_v1_ckdepi<-1.2
pc1<-2.3
pc2<-3.4
pc3<-4.5
V1AGE01<-27
GENDER<-"F"
Before embarking on the loop, I think you have confused the "name of
the function", which is "Score", with the return value of the
function. I don't think you want to change the function's name or it
won't work unless you change the name in the function call. Therefore,
I am going to make a blind guess and assume that you want the name of
the return value of the function to be the rowname for the value that
is used in the function.
Now you can do something like this:
for(i in 1:nrow(met)) {
x<-Scores(Z=metalofGT,formula="met[i]~egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+GENDER")
names(x)<-names(met)[i]
filename<-paste("prep",i,".Rdata",sep="")
save(x, file=filename, compress="bzip2")
}
This will produce five files with the names you requested, each
containing whatever value the function "Score" produces. The name of
that value will be the rowname of "met" that produced it.
Jim
On Fri, Jul 3, 2015 at 2:48 AM, Lida Zeighami <lid.zigh at gmail.com>
wrote:> Thank you so much for replying me!
> for better understanding my problem, I explain my problem more:
>
> I have a 682*1 matrix called "met" , the first 5 rows similar
below:
>
>> rownames(met)[1:5]
>
> [1] "glycine_imp"
> [2] "Nacetylglycine_imp"
> [3] "sarcosine_imp"
> [4] "dimethylglycine_imp"
> [5] "betaine_imp"
>
> and I have a function in R that each time use one of the row names of
"met"
> matrix and create a new object file and I should save the objects!
>
> my function is "
>
Scores(Z=metalofGT,formula="met[i]~egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+GENDER")
> " that each time just I should change the met[i] and replace by row
names
> "met" one by one and for each of them I should rename the
function and
> after that I should save each object!
> for example for first row of "met" I have
>
>> prep1<-
Scores(Z=metalofGT,formula="glycine_imp~egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+GENDER")
> #creat the object file for first row and called prep1###
>
>> save(prep1, file="prep1.RData", compress="bzip2")
##save the
> object file as "prep1.RData"#####
>
> I should do this process for 682 row names of "met" matrix and at
the end I
> should have "prep1.RData" , "prep2.RData" ,
"prep3.RData"
>
> so, would you please help me how to do it?
>
> Many Thanks,
> Ati
>
> On Wed, Jul 1, 2015 at 1:07 PM, Lida Zeighami <lid.zigh at gmail.com>
wrote:
>
>> I have 682 variables in a data frame , and a function that I should
feed
>> 682 variables in this function one by one and each time save the file
as a
>> special name!
>> for emaple:
>> my data frame file includes 682 names :
>> 1 aaa
>> 2 bbb
>> 3 dfdsfg
>> 4 fghh
>> .
>>
>> 682 fgfhg
>> and a function like prep(Z, aaa, .....) and each time I should change
the
>> variable name in this function and read the variable from the data
frame
>> and each time I should save the file as a special name such as:
>>
>> prep1<- prep(z, aaa,...)
>> prep2<- prep(z, bbb,...)
>> prep3<- prep(z, dfdsfg,..)
>> Prep4<- prep(z, fghh,...)
>>
>> How can I use loop function in R to that?
>>
>> Thanks
>>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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.
Lida,
I expect that there is a better way to solve your problem than the process you
propose.
However, something like this may do what you want.
###
## met <- read.csv("your_met_file?)
## Since I do not have your file a made a small 5*1 character vector.
met <- c("glycine_imp",
"Nacetylglycine_imp",
"sarcosine_imp",
"dimethylglycine_imp",
"betaine_imp")
for (i in seq_along(met)) {
my_formula <- paste0(met[i],
"~egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+GENDER")
prep <- Scores(Z=metalofGT, formula = my_formula)
save(prep, file = paste0("prep", i))
}
###
Mark
R. Mark Sharp, Ph.D.
Director of Primate Records Database
Southwest National Primate Research Center
Texas Biomedical Research Institute
P.O. Box 760549
San Antonio, TX 78245-0549
Telephone: (210)258-9476
e-mail: msharp at TxBiomed.org
> On Jul 2, 2015, at 11:48 AM, Lida Zeighami <lid.zigh at gmail.com>
wrote:
>
> Thank you so much for replying me!
> for better understanding my problem, I explain my problem more:
>
> I have a 682*1 matrix called "met" , the first 5 rows similar
below:
>
>> rownames(met)[1:5]
>
> [1] "glycine_imp"
> [2] "Nacetylglycine_imp"
> [3] "sarcosine_imp"
> [4] "dimethylglycine_imp"
> [5] "betaine_imp"
>
> and I have a function in R that each time use one of the row names of
"met"
> matrix and create a new object file and I should save the objects!
>
> my function is "
>
Scores(Z=metalofGT,formula="met[i]~egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+GENDER")
> " that each time just I should change the met[i] and replace by row
names
> "met" one by one and for each of them I should rename the
function and
> after that I should save each object!
> for example for first row of "met" I have
>
>> prep1<-
Scores(Z=metalofGT,formula="glycine_imp~egfr_v1_ckdepi+pc1+pc2+pc3+V1AGE01+GENDER")
> #creat the object file for first row and called prep1###
>
>> save(prep1, file="prep1.RData", compress="bzip2")
##save the
> object file as "prep1.RData"#####
>
> I should do this process for 682 row names of "met" matrix and at
the end I
> should have "prep1.RData" , "prep2.RData" ,
"prep3.RData"
>
> so, would you please help me how to do it?
>
> Many Thanks,
> Ati
>
> On Wed, Jul 1, 2015 at 1:07 PM, Lida Zeighami <lid.zigh at gmail.com>
wrote:
>
>> I have 682 variables in a data frame , and a function that I should
feed
>> 682 variables in this function one by one and each time save the file
as a
>> special name!
>> for emaple:
>> my data frame file includes 682 names :
>> 1 aaa
>> 2 bbb
>> 3 dfdsfg
>> 4 fghh
>> .
>>
>> 682 fgfhg
>> and a function like prep(Z, aaa, .....) and each time I should change
the
>> variable name in this function and read the variable from the data
frame
>> and each time I should save the file as a special name such as:
>>
>> prep1<- prep(z, aaa,...)
>> prep2<- prep(z, bbb,...)
>> prep3<- prep(z, dfdsfg,..)
>> Prep4<- prep(z, fghh,...)
>>
>> How can I use loop function in R to that?
>>
>> Thanks
>>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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.