R help - Jan 2011 - problem reading file containing bit vector

Hi I have a tab delimited file with fillowing content:

"swissProtID"    "entrezID"    "bitVec"
"Q62924"             "---"   
"00000000100010000000000000000000"
"P18897"             "---"   
"00000000000001000100000000000000"
"Q62736"             "---"   
"00001000001000000000001000000000"
"P13589"             "---"   
"00100000010000010000000000000000"

When I read this the bitVec field is not read properly. Instead, the value
showing is "Inf" .
How should i read this file?  as.is/colclasses field in read function is not
helping me.

Is there any package that can do bitwise operation(and/or) on bitVectors.
bitops seems to do that but I need output in bitvector format only.
Thanks
Fahim


-- 
Fahim Mohammad
Bioinforformatics Lab
University of Louisville
Louisville, KY, USA
Ph:  +1-502-409-1167

	[[alternative HTML version deleted]]

On Jan 30, 2011, at 12:22 PM, Fahim M wrote:
> Hi I have a tab delimited file with fillowing content:
>
> "swissProtID"    "entrezID"    "bitVec"
> "Q62924"             "---"   
"00000000100010000000000000000000"
> "P18897"             "---"   
"00000000000001000100000000000000"
> "Q62736"             "---"   
"00001000001000000000001000000000"
> "P13589"             "---"   
"00100000010000010000000000000000"
>
> When I read this the bitVec field is not read properly. Instead, the  
> value
> showing is "Inf" .
> How should i read this file?  as.is/colclasses field in read  
> function is not
> helping me.
"Not helping"? Show your code.
>
> Is there any package that can do bitwise operation(and/or) on  
> bitVectors.
> bitops seems to do that but I need output in bitvector format only.
> Thanks
> Fahim
>
>
> -- 
> Fahim Mohammad
> Bioinforformatics Lab
> University of Louisville

David Winsemius, MD
West Hartford, CT

I think you want to make sure you read it is as character:
> x <- read.table(textConnection('"swissProtID"   
"entrezID"    "bitVec"
+ "Q62924"             "---"   
"00000000100010000000000000000000"
+ "P18897"             "---"   
"00000000000001000100000000000000"
+ "Q62736"             "---"   
"00001000001000000000001000000000"
+ "P13589"             "---"   
"00100000010000010000000000000000"')
+     , colClasses = rep('character', 3)
+     , as.is = TRUE
+     , header = TRUE
+     )
> closeAllConnections()
>
> x
  swissProtID entrezID                           bitVec
1      Q62924      --- 00000000100010000000000000000000
2      P18897      --- 00000000000001000100000000000000
3      Q62736      --- 00001000001000000000001000000000
4      P13589      --- 00100000010000010000000000000000
> str(x)
'data.frame':   4 obs. of  3 variables:
 $ swissProtID: chr  "Q62924" "P18897" "Q62736"
"P13589"
 $ entrezID   : chr  "---" "---" "---"
"---"
 $ bitVec     : chr  "00000000100010000000000000000000"
"00000000000001000100000000000000"
"00001000001000000000001000000000"
"00100000010000010000000000000000"
>

On Sun, Jan 30, 2011 at 12:22 PM, Fahim M <fahim.md at gmail.com>
wrote:
> Hi I have a tab delimited file with fillowing content:
>
> "swissProtID" ? ?"entrezID" ? ?"bitVec"
> "Q62924" ? ? ? ? ? ? "---" ?
?"00000000100010000000000000000000"
> "P18897" ? ? ? ? ? ? "---" ?
?"00000000000001000100000000000000"
> "Q62736" ? ? ? ? ? ? "---" ?
?"00001000001000000000001000000000"
> "P13589" ? ? ? ? ? ? "---" ?
?"00100000010000010000000000000000"
>
> When I read this the bitVec field is not read properly. Instead, the value
> showing is "Inf" .
> How should i read this file? ?as.is/colclasses field in read function is
not
> helping me.
>
> Is there any package that can do bitwise operation(and/or) on bitVectors.
> bitops seems to do that but I need output in bitvector format only.
> Thanks
> Fahim
>
>
> --
> Fahim Mohammad
> Bioinforformatics Lab
> University of Louisville
> Louisville, KY, USA
> Ph: ?+1-502-409-1167
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
>


-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?