0

I have 3 data variables created in R with the following information in each Variable 1: coordinate

x   y 
0.1 0.1

Variable 2: mz

100.0 
100.1 
100.2 
100.3 
....
....
999.9

Variable 3: intensity

4.533154e-01  
2.997068e-01  
4.542300e-01  
2.905961e-01  
4.636095e-01
.....
.....

Now I want to export this information as a text file. Such that I have the following format

 x   y 
0.1 0.1 
100.0   2.905961e-01 
100.1   4.533154e-01  
100.2   2.997068e-01 
100.3   4.542300e-01 
....
....
999.9   2.905961e-01

I wrote the following code for this in R:

spectralData<-cbind(mz, intensity, deparse.level = 0)
foo<-c('%2.1f', '%2.8f')
cbar<-sapply(1:2,function(j) sprintf(foo[j],spectralData[,j]))
write(t(cbar),'/Desktop/cbar.txt',ncolumns=2)

data<-rbind(coordinate,spectralData,deparse.level = 0)
write.table(data, "/Desktop/test.txt", row.names = FALSE)

I receive the text file but with it has two issues. First, I get row numbers as an additional column. How should I avoid this? Second, the precision of the numbers changes for both mz and intensity columns. How can I get the same precision after decimal? Here is what the exported data looks like

"x" "y"
"1" 0.100000001490116 0.100000001490116
"2" 100 -1.77635683940025e-15
"3" 100.099998474121 0.0266907754084524
"4" 100.199996948242 0.0533815508169102
"5" 100.300003051758 3.5527136788005e-15
"6" 100.400001525879 0.135286505970676
"7" 100.5 0.0286329399926419
novicegeek
  • 773
  • 2
  • 9
  • 29

2 Answers2

2

To avoid row numbers use this -

write.table(data, "/Desktop/test.txt",row.names = FALSE)
RHelp
  • 815
  • 2
  • 8
  • 23
2

If you want specific precisions for each column (part of your question, I believe), one way is to start by running your data frame through a sprintf statement to create an array of character strings. Then use write to write the data to a file -- the quote marks will not be carried thru. Here's an example.

fbar<-sin((1:10)/10)
fbar<-matrix(fbar,5)
#fbar
#           [,1]      [,2]
#[1,] 0.09983342 0.5646425
#[2,] 0.19866933 0.6442177
#[3,] 0.29552021 0.7173561
#[4,] 0.38941834 0.7833269
#[5,] 0.47942554 0.8414710
foo<-c('%2.8f', '%2.3f')
cbar<-sapply(1:2,function(j) sprintf(foo[j],fbar[,j]) )
write(t(cbar),'cbar.txt',ncolumns=2)
#cbar
#0.09983342 0.565
#0.19866933 0.644
#0.29552021 0.717
#0.38941834 0.783
#0.47942554 0.841
Carl Witthoft
  • 20,573
  • 9
  • 43
  • 73
  • I did this and it works! Now how do I append the coordinate information above the two columns in the same file. I have made changes in the above code according to your suggestion. – novicegeek May 19 '14 at 13:46
  • If by "coord info" you mean the column names "x" and "y", a simple approach is `write(c(' x ',' y '),'cbar.txt',ncolumns=2)` with appropriate spacing between the labels, followed with `write(t(cbar),'cbar.txt',ncolumns=2,append=TRUE)` . – Carl Witthoft May 19 '14 at 14:13
  • The coordinate information is the first variable which consists of two lines "x" "y" in line 1 and the values of x and y in the second line. This coordinate variable should be the first two lines of the file and then the m/z and intensity values (2 columns) would start. – novicegeek May 19 '14 at 14:16
  • 1
    OK, same suggestion, but use your choice of `write`, `write.table`, etc. for the first two lines of text, then the final `write(....,append=TRUE)` – Carl Witthoft May 19 '14 at 14:17