[R] subsetting data file by intoducing a second file

[arun]

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,
Ö

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