Skip to content

question

10 messages · Calin Uioreanu, jim holtman, Lida Zeighami +3 more

Original
Lida Zeighami
# 
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
Calin Uioreanu
# 
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:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      jim holtman
    

    

      
      #
    

  


  

      
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:

        

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      jim holtman
    

    

      
      #
    

  


  

      
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:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Lida Zeighami
    

    

      
      #
    

  


  

      
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:

            

      
      
      
    

        
[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

            

      
      
      
    

        
#creat the object file for first row and called prep1###

            

      
      
      
    

        
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:

        

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      PIKAL Petr
    

    

      
      #
    

  


  

      
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

            

      
      
      
    

        

      
      
    

        
________________________________
Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m.
Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu.
Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat.
Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu.

V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?:
- vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu.
- a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou.
- trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech.
- odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?.

This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system.
If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner.
The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email.

In case that this e-mail forms part of business dealings:
- the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning.
- if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation.
- the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects.
- the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient.

  
  


  


      

    

    

      
      

        


  

        

      Jim Lemon
    

    

      
      #
    

  


  

      
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:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Mark Sharp
    

    

      
      #
    

  


  

      
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

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
2 days later

    

      
      

        


  

        

      Lida Zeighami
    

    

      
      #
    

  


  

      
Hi Mark,

Thank you so much for your help.

I run your code and it works great for 5*1 character vector but if I run it
for 682*1 character vector it has some error like this:

Error in model.frame.default(formula = formula, ...) :
  variable lengths differ (found for 'egfr_v1_ckdepi')

Would you please let me know what's the reason is?

Many Thanks,
Lida

        
On Fri, Jul 3, 2015 at 11:38 PM, Mark Sharp <msharp at txbiomed.org> wrote:

        

            

      
      
      
    

        

      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Mark Sharp
    

    

      
      #
    

  


  

      
Lida,

Please send the code that you ran. It is almost certain that you have a vector being formed that is the wrong length. There should be only one vector that you use to increment through the loop and that is the character vector formed when you read in your_met_file to form the met character vector.

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