R help - Jan 2008 - numerical data frame

Dear All,
   
  I've successfully import my synteny data to R by using scan command. Below
show my results. My major problem with my data is how am i going to combine the
column names with the data( splt) where i have tried on cbind but a warning
message occur. I have realized that the splt data only have 5 column instead of
6. Please help me with this!!
   
  I want my data to be a numerical data with a proper column and column names
and to  replace CS with 1 and CSO with 0 and also to get remove all the
punctuations and the characters from the data.
   
  Attach herewith is my original data. Your kindly help is highly appreciated
and thanks in advance.
   
  Cheers,
  Anisah
   
   
   
  1)for col names
   
 
nms<-scan("C:/Users/user/Documents/cfa-1.txt",sep="\t",nlines=1,skip=10,what=character(0))
Read 6 items
> nms
[1] "CS(O) id (number of marker/anchor) "                   
[2] " Location(s) on reference "                            
[3] "CS(O) size"                                            
[4] "CS(O) density on reference chromosome"                 
[5] "Location(s) on tested  "                               
[6] "Breakpoints CS(O) locations (denstiy of marker/anchor)"
  
2) my data
   
 
x<-scan("C:/Users/user/Documents/cfa-1.txt",sep="\n",skip=12,what=character(0))
Read 21 items
> splt<-strsplit(x,"\t")
> splt
[[1]]
[1] "CS 1 (73): "                       " cfa1: [ 3251712 -
24126920 ] "
[3] "  20875208 "                       " 3 "
[5] " hsa18: [ 132170848 - 50139168 ] " "] 24126920, 24153560 [(8
) "
  [[2]]
[1] "CS 2 (3): "                       " cfa1: [ 24153560 -
24265894 ] "
[3] "  112334 "                        " 27 "
[5] " hsa18: [ 50105060 - 49934572 ] " "] 24265894, 24823786 [(7
) "
  [[3]]
[1] "CSO 3.1 (6): "
[2] " cfa1: [ 24823786 - 27113036 ] "
[3] "  2289250 "
[4] " 3  "
[5] " hsa18: [ 48121156 - 46579500 ]- Decreasing order - ] 27113036,
27418228 [ (13)"
  [[4]]
[1] "CSO 3.2 (4): "
[2] " cfa1: [ 27418228 - 27578150 ] "
[3] "  159922 "
[4] " 25  "
[5] " hsa18: [ 13872043 - 13208795 ]- Decreasing order - ] 27578150,
28055666 [(9 ) "
  [[5]]
[1] "CS 4 (4): "                        " cfa1: [ 28055666 -
28835230 ] "
[3] "  779564 "                         " 5 "
[5] " hsa6: [ 132311008 - 133132200 ] " "] 28835230, 29482792 [(7
) "
  [[6]]
[1] "CS 5 (46): "                       " cfa1: [ 29482792 -
40120672 ] "
[3] "  10637880 "                       " 4 "
[5] " hsa6: [ 133604208 - 146227152 ] " "] 40120672, 40539680 [(8
) "
  [[7]]
[1] "CS 6 (9): "                        " cfa1: [ 40539680 -
43339444 ] "
[3] "  2799764 "                        " 3 "
[5] " hsa6: [ 146390608 - 149867328 ] " "] 43339444, 43390788
[(13 ) "
  [[8]]
[1] "CSO 7.1 (74): "
[2] " cfa1: [ 43390788 - 59714992 ] "
[3] "  16324204 "
[4] " 5  "
[5] " hsa6: [ 149929104 - 169714432 ]- Increasing order -] 59714992,
59864308 [ (15)"
  [[9]]
[1] "CSO 7.2 (52): "                                        
[2] " cfa1: [ 59864308 - 72417520 ] "                       
[3] "  12553212 "                                           
[4] " 4  "                                                  
[5] " hsa6: [ 116707976 - 131508152 ]- Increasing order -  "
[6] "] 72417520, 73256040 [(7 ) "                           
  [[10]]
[1] "CSO 8.1 (12): "                                     
[2] " cfa1: [ 73256040 - 75192808 ] "                    
[3] "  1936768 "                                         
[4] " 6  "                                               
[5] " hsa9: [ 98441680 - 96360824 ]- Decreasing order - "
[6] "] 75192808, 75272528 [ "                            
[7] " (6 )"                                              
  [[11]]
[1] "CSO 8.2 (56): "                                     
[2] " cfa1: [ 75272528 - 91881664 ] "                    
[3] "  16609136 "                                        
[4] " 3  "                                               
[5] " hsa9: [ 89530256 - 70341312 ]- Decreasing order - "
[6] "] 91881664, 92281272 [ "                            
[7] " (5 )"                                              
  [[12]]
[1] "CSO 8.3 (22): "                                   
[2] " cfa1: [ 92281272 - 96913624 ] "                  
[3] "  4632352 "                                       
[4] " 5  "                                             
[5] " hsa9: [ 261625 - 5755076 ]- Increasing order -  "
[6] "] 96913624, 98067040 [ "                          
[7] " (5 )"                                            
  [[13]]
[1] "CSO 8.4 (15): "
[2] " cfa1: [ 98067040 - 100692560 ]   2625520 "
[3] " 6  "
[4] " hsa9: [ 93833248 - 89771184 ]- Decreasing order - ] 100692560,
101013264 [ "
[5] "(13 )"
  [[14]]
[1] "CSO 8.5 (18): "
[2] " cfa1: [ 101013264 - 102120080 ]  1106816 "
[3] " 16  "
[4] " hsa9: [ 95832896 - 94012312 ]- Decreasing order -]
102271920,102458192 [(25 ) "
  [[15]]
[1] "CS 9 (55): "                               
[2] " cfa1: [ 102458192 - 105936824 ]  3478632 "
[3] " 16 "                                      
[4] " hsa19: [ 63765096 - 59618416 ] "          
[5] "] 105936824, 106097392 [(35 ) "            
  [[16]]
[1] "CSO 10.1 (81): "                                     
[2] " cfa1: [ 106097392 - 110263696 ]  4166304 "          
[3] " 19  "                                               
[4] " hsa19: [ 59386008 - 54256216 ]- Decreasing order - "
[5] "] 110263696,110288752 [ (60 )"                       
  [[17]]
[1] "CSO 10.2 (18): "                                     
[2] " cfa1: [ 110288752 - 110567608 ]  278856 "           
[3] " 65  "                                               
[4] " hsa19: [ 54163196 - 53814360 ]- Decreasing order - "
[5] "] 110567608,110575576 [ (50 )"                       
  [[18]]
[1] "CSO 10.3 (60): "                                     
[2] " cfa1: [ 110575576 - 112727048 ]  2151472 "          
[3] " 28  "                                               
[4] " hsa19: [ 53649284 - 50959884 ]- Decreasing order - "
[5] "] 112727048,112775144 [(40 ) "                       
  [[19]]
[1] "CS 11 (173): "                             
[2] " cfa1: [ 112775144 - 119848336 ]  7073192 "
[3] " 24 "                                      
[4] " hsa19: [ 50887772 - 40849556 ] "          
[5] "] 119848336, 119880560 [(55 ) "            
  [[20]]
[1] "CS 12 (33): "                              
[2] " cfa1: [ 119880560 - 121690672 ]  1810112 "
[3] " 18 "                                      
[4] " hsa19: [ 40824500 - 38556448 ] "          
[5] "] 121690672, 121820640 [(16 ) "            
  [[21]]
[1] "CS 13 (22): "                              
[2] " cfa1: [ 121820640 - 124798800 ]  2978160 "
[3] " 7 "                                       
[4] " hsa19: [ 38391408 - 34709332 ] "          
[5] "] 124798800, Telomere [(-NA-) "            
   

       
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>   I've successfully import my synteny data to R by using scan 
> command. Below show my results. My major problem with my data is how
> am i going to combine the column names with the data( splt) where i 
> have tried on cbind but a warning message occur. I have realized 
> that the splt data only have 5 column instead of 6. Please help me with 
this!!
> 
>   I want my data to be a numerical data with a proper column and 
> column names and to  replace CS with 1 and CSO with 0 and also to 
> get remove all the punctuations and the characters from the data.
>   1)for col names
> 
>  
nms<-scan("C:/Users/user/Documents/cfa-1.txt",sep="\t",nlines=1,
> skip=10,what=character(0))
> Read 6 items
> > nms
> [1] "CS(O) id (number of marker/anchor) " 
> [2] " Location(s) on reference " 
> [3] "CS(O) size" 
> [4] "CS(O) density on reference chromosome" 
> [5] "Location(s) on tested  " 
> [6] "Breakpoints CS(O) locations (denstiy of marker/anchor)"
> 
> 2) my data
> 
>  
x<-scan("C:/Users/user/Documents/cfa-1.txt",sep="\n",skip=12,
> what=character(0))
> Read 21 items
> > splt<-strsplit(x,"\t")
> > splt
> [[1]]
> [1] "CS 1 (73): "                       " cfa1: [ 3251712 -
24126920 ] "
 
> [3] "  20875208 "                       " 3 "  
> [5] " hsa18: [ 132170848 - 50139168 ] " "] 24126920,
24153560 [(8 ) "
>   [[2]]
> [1] "CS 2 (3): "                       " cfa1: [ 24153560 -
24265894 ] "
> [3] "  112334 "                        " 27 " 
> [5] " hsa18: [ 50105060 - 49934572 ] " "] 24265894, 24823786
[(7 ) "
>   [[3]]
> [1] "CSO 3.1 (6): "  
> [2] " cfa1: [ 24823786 - 27113036 ] "  
> [3] "  2289250 "  
> [4] " 3  "  
> [5] " hsa18: [ 48121156 - 46579500 ]- Decreasing order - ] 27113036,
> 27418228 [ (13)"
> ...
You are probably better off using read.table or read.delim to get your 
data into R, since you most likely want it in the form of a data frame 
rather than a list.

Otherwise,try this.
#Convert to matrix
datamat <- matrix(unlist(splt),  ncol=6, byrow=TRUE)

#This will remove punctuation, but it looks like you want to do something 
more with some of the columns; I'm just not sure what it is.
nopunct <- gsub("[[:punct:]]", "", datamat) 

#Convert to a data frame
df <- as.data.frame(nopunct)

#Make column 3 numeric (you will probably want to do something like this 
for each one)
df[,3] <- as.numeric(df[,3])

# Set column names
names(df) <- nms

Regards,
Richie.

Mathematical Sciences Unit
HSL


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