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Ozgul Inceoglu

2013-Feb-12 14:29 UTC

[R] subsetting data file by intoducing a second file

Hello,

I have a very data matrix and I have a file which has the names that I need to
subset. However I cannot manage to subset the main file. ANy idea?

bg <- read.table (file.choose(), header=T, row.names)
bg
          Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125
Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209
Otu00218
Gi20Jun11  0.001217        0 0.001217        0 0.000000        0        0       
0 0.001217        0        0        0        0        0 0.001217        0
0.001217
Gi40Jun11  0.000000        0 0.000000        0 0.000000        0        0       
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
Gi425Jun11 0.000000        0 0.000000        0 0.000000        0        0       
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
Gi45Jun11  0.000000        0 0.000000        0 0.001513        0        0       
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
Gi475Jun11 0.000000        0 0.000000        0 0.000000        0        0       
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
Gi50Jun11  0.000000        0 0.000000        0 0.000000        0        0       
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
...
#second file which has the names that I want to subset
c_bg
      [,1]     
  [1,] "Otu0128"
  [2,] "Otu0218"
  [3,] "Otu0034"
  [4,] "Otu0257"
  [5,] "Otu0212"
  [6,] "Otu0279"
  [7,] "Otu0318"
  [8,] "Otu0266"
  [9,] "Otu0056"
...
#by using the c_bg name file, I would like to subset bg file

g1<-subset(bg,colnames(bg) %in% (c_bg))

# this returns me the all the column names in bg file.

Thank you,
?

arun

2013-Feb-12 15:14 UTC

head link

[R] subsetting data file by intoducing a second file

Hi,


bg<- read.table(text="
???? Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131
Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209 Otu00218
Gi20Jun11? 0.001217??????? 0 0.001217??????? 0 0.000000??????? 0??????? 0???????
0 0.001217??????? 0??????? 0??????? 0??????? 0??????? 0 0.001217??????? 0
0.001217
Gi40Jun11? 0.000000??????? 0 0.000000??????? 0 0.000000??????? 0??????? 0???????
0 0.000000??????? 0??????? 0??????? 0??????? 0??????? 0 0.000000??????? 0
0.000000
Gi425Jun11 0.000000??????? 0 0.000000??????? 0 0.000000??????? 0??????? 0???????
0 0.000000??????? 0??????? 0??????? 0??????? 0??????? 0 0.000000??????? 0
0.000000
Gi45Jun11? 0.000000??????? 0 0.000000??????? 0 0.001513??????? 0??????? 0???????
0 0.000000??????? 0??????? 0??????? 0??????? 0??????? 0 0.000000??????? 0
0.000000
Gi475Jun11 0.000000??????? 0 0.000000??????? 0 0.000000??????? 0??????? 0???????
0 0.000000??????? 0??????? 0??????? 0??????? 0??????? 0 0.000000??????? 0
0.000000
Gi50Jun11? 0.000000??????? 0 0.000000??????? 0 0.000000??????? 0??????? 0???????
0 0.000000??????? 0??????? 0??????? 0??????? 0??????? 0 0.000000??????? 0
0.000000
",sep="",header=TRUE,stringsAsFactors=F)

c_bg<- read.table(text="
?Otu00039
?Otu0128
?Otu0218
?Otu0034
?Otu00158
? Otu0257
? Otu0212
? Otu00125
? ",sep="",header=FALSE,stringsAsFactors=F)
bg[,names(bg)%in%c_bg[,1]]
?# ???????? Otu00039 Otu00125 Otu00158
#Gi20Jun11? 0.001217??????? 0??????? 0
#Gi40Jun11? 0.000000??????? 0??????? 0
#Gi425Jun11 0.000000??????? 0??????? 0
#Gi45Jun11? 0.000000??????? 0??????? 0
#Gi475Jun11 0.000000??????? 0??????? 0
#Gi50Jun11? 0.000000??????? 0??????? 0


A.K.



----- Original Message -----
From: Ozgul Inceoglu <Ozgul.Inceoglu at ulb.ac.be>
To: r-help at r-project.org
Cc: 
Sent: Tuesday, February 12, 2013 9:29 AM
Subject: [R] subsetting data file by intoducing a second file

Hello,

I have a very data matrix and I have a file which has the names that I need to
subset. However I cannot manage to subset the main file. ANy idea?

bg <- read.table (file.choose(), header=T, row.names)
bg
? ? ? ? ? Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125
Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209
Otu00218
Gi20Jun11? 0.001217? ? ? ? 0 0.001217? ? ? ? 0 0.000000? ? ? ? 0? ? ? ? 0? ? ? ?
0 0.001217? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0 0.001217? ? ? ? 0
0.001217
Gi40Jun11? 0.000000? ? ? ? 0 0.000000? ? ? ? 0 0.000000? ? ? ? 0? ? ? ? 0? ? ? ?
0 0.000000? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0 0.000000? ? ? ? 0
0.000000
Gi425Jun11 0.000000? ? ? ? 0 0.000000? ? ? ? 0 0.000000? ? ? ? 0? ? ? ? 0? ? ? ?
0 0.000000? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0 0.000000? ? ? ? 0
0.000000
Gi45Jun11? 0.000000? ? ? ? 0 0.000000? ? ? ? 0 0.001513? ? ? ? 0? ? ? ? 0? ? ? ?
0 0.000000? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0 0.000000? ? ? ? 0
0.000000
Gi475Jun11 0.000000? ? ? ? 0 0.000000? ? ? ? 0 0.000000? ? ? ? 0? ? ? ? 0? ? ? ?
0 0.000000? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0 0.000000? ? ? ? 0
0.000000
Gi50Jun11? 0.000000? ? ? ? 0 0.000000? ? ? ? 0 0.000000? ? ? ? 0? ? ? ? 0? ? ? ?
0 0.000000? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0? ? ? ? 0 0.000000? ? ? ? 0
0.000000
...
#second file which has the names that I want to subset
c_bg
? ? ? [,1]? ? 
? [1,] "Otu0128"
? [2,] "Otu0218"
? [3,] "Otu0034"
? [4,] "Otu0257"
? [5,] "Otu0212"
? [6,] "Otu0279"
? [7,] "Otu0318"
? [8,] "Otu0266"
? [9,] "Otu0056"
...
#by using the c_bg name file, I would like to subset bg file

g1<-subset(bg,colnames(bg) %in% (c_bg))

# this returns me the all the column names in bg file.

Thank you,
?

______________________________________________
R-help at r-project.org mailing list
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.

Rui Barradas

2013-Feb-12 16:48 UTC

head link

[R] subsetting data file by intoducing a second file

Hello,

Read the help page ?subset more carefully, it's argument 'select'
you
should be using:

subset(bg, select = c_bg)


Hope this helps,

Rui Barradas

Em 12-02-2013 14:29, Ozgul Inceoglu escreveu:> Hello,
>
> I have a very data matrix and I have a file which has the names that I need
to subset. However I cannot manage to subset the main file. ANy idea?
>
> bg <- read.table (file.choose(), header=T, row.names)
> bg
>            Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125
Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209
Otu00218
> Gi20Jun11  0.001217        0 0.001217        0 0.000000        0        0  
0 0.001217        0        0        0        0        0 0.001217        0
0.001217
> Gi40Jun11  0.000000        0 0.000000        0 0.000000        0        0  
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
> Gi425Jun11 0.000000        0 0.000000        0 0.000000        0        0  
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
> Gi45Jun11  0.000000        0 0.000000        0 0.001513        0        0  
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
> Gi475Jun11 0.000000        0 0.000000        0 0.000000        0        0  
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
> Gi50Jun11  0.000000        0 0.000000        0 0.000000        0        0  
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
> ...
> #second file which has the names that I want to subset
> c_bg
>        [,1]
>    [1,] "Otu0128"
>    [2,] "Otu0218"
>    [3,] "Otu0034"
>    [4,] "Otu0257"
>    [5,] "Otu0212"
>    [6,] "Otu0279"
>    [7,] "Otu0318"
>    [8,] "Otu0266"
>    [9,] "Otu0056"
> ...
> #by using the c_bg name file, I would like to subset bg file
>
> g1<-subset(bg,colnames(bg) %in% (c_bg))
>
> # this returns me the all the column names in bg file.
>
> Thank you,
> ?
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
>

Eik Vettorazzi

2013-Feb-12 16:49 UTC

head link

[R] subsetting data file by intoducing a second file

Hi Ozgul,
the interesting part is the "select" parameter in subset:

subset(bg,select=c_bg[,1])


cheers

Am 12.02.2013 15:29, schrieb Ozgul Inceoglu:> Hello,
> 
> I have a very data matrix and I have a file which has the names that I need
to subset. However I cannot manage to subset the main file. ANy idea?
> 
> bg <- read.table (file.choose(), header=T, row.names)
> bg
>           Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125
Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209
Otu00218
> Gi20Jun11  0.001217        0 0.001217        0 0.000000        0        0  
0 0.001217        0        0        0        0        0 0.001217        0
0.001217
> Gi40Jun11  0.000000        0 0.000000        0 0.000000        0        0  
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
> Gi425Jun11 0.000000        0 0.000000        0 0.000000        0        0  
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
> Gi45Jun11  0.000000        0 0.000000        0 0.001513        0        0  
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
> Gi475Jun11 0.000000        0 0.000000        0 0.000000        0        0  
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
> Gi50Jun11  0.000000        0 0.000000        0 0.000000        0        0  
0 0.000000        0        0        0        0        0 0.000000        0
0.000000
> ...
> #second file which has the names that I want to subset
> c_bg
>       [,1]     
>   [1,] "Otu0128"
>   [2,] "Otu0218"
>   [3,] "Otu0034"
>   [4,] "Otu0257"
>   [5,] "Otu0212"
>   [6,] "Otu0279"
>   [7,] "Otu0318"
>   [8,] "Otu0266"
>   [9,] "Otu0056"
> ...
> #by using the c_bg name file, I would like to subset bg file
> 
> g1<-subset(bg,colnames(bg) %in% (c_bg))
> 
> # this returns me the all the column names in bg file.
> 
> Thank you,
> ?
> 
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
> 

-- 
Eik Vettorazzi
Institut f?r Medizinische Biometrie und Epidemiologie
Universit?tsklinikum Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

T ++49/40/7410-58243
F ++49/40/7410-57790
--
Pflichtangaben gem?? Gesetz ?ber elektronische Handelsregister und
Genossenschaftsregister sowie das Unternehmensregister (EHUG):

Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts;
Gerichtsstand: Hamburg

Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Dr. Alexander
Kirstein, Joachim Pr?l?, Prof. Dr. Dr. Uwe Koch-Gromus

R help - Feb 2013 - subsetting data file by intoducing a second file

[R] subsetting data file by intoducing a second file

[R] subsetting data file by intoducing a second file

[R] subsetting data file by intoducing a second file

[R] subsetting data file by intoducing a second file

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