[R] For help in R coding

[David Winsemius]

On Jul 4, 2011, at 1:29 PM, Bansal, Vikas wrote:

> Dear sir,
>
> I have one more problem.Sorry to disturb you again.
>
> I have a data frame like this-
>
> Col1     Col2             Col3                  Col4
> 1             0                  1                        4
> 0             0                  0                        2
> 4              2                 0                        0
> 1              5                 0                        0
> 0              0                 4                        3
> 0               0                 0                        2
> 0               0                 0                        0
> 1               1                 0                        5
>
> I want to delete all those rows which have more than two 0s
> like in above input  row2 has 3 zeros,row6 has 3 zeros and row 7 has  
> 4 zeros.so i want to exclude them so that my output should be-
>
> Col1     Col2             Col3                  Col4
> 1             0                  1                        4
> 4              2                 0                        0
> 1              5                 0                        0
> 0              0                 4                        3
> 1               1                 0                        5
>
> Can you please tell me how to code for this problem?

I am having a difficult time figuring out why this is not an obvious  
application for `apply` and "[" using logical indexing. I suggest you  
do some more self-study with the introductory material that you will  
find here:

http://cran.r-project.org/other-docs.html

(It also is a frequently asked question, so searching the archives for  
worked examples should also be considered.)

Using search terms "delete all rows with =="

http://search.r-project.org/cgi-bin/namazu.cgi?query=delete+rows+with+all+%3D%3D&max=100&result=normal&sort=score&idxname=functions&idxname=Rhelp08&idxname=Rhelp10&idxname=Rhelp02


-- 
David.

>
>
>
>
>
>
> Thanking you,
> Warm Regards
> Vikas Bansal
> Msc Bioinformatics
> Kings College London
> ________________________________________
> From: David Winsemius [dwinsemius at comcast.net]
> Sent: Monday, July 04, 2011 2:02 AM
> To: Bansal, Vikas
> Cc: Dennis Murphy; r-help at r-project.org
> Subject: Re: [R] For help in R coding
>
> On Jul 3, 2011, at 6:10 PM, Bansal, Vikas wrote:
>
>>> So I want to code so that it will give the output like this-
>>>
>>> DATA FRAME (Input)
>
> Editing the task so it is reproducible:
>
> dat <- read.table(textConnection(' col3                 col9
>   T                      .a,g,,
>   A                    .t,t,,
>   A                    .,c,c,
>   C                     .,a,,,
>   G                     .,t,t,t
>   A                     .c,,g,^!.
>   A                      .g,ggg.^!,
>   A                      .$,,,,,.,
>   C                      a,g,,t,
>   T                      ,,,,,.,^!.
>   T                       ,$,,,,.,."'), header=TRUE,
> stringsAsFactors=FALSE)
>
>>> output
>>>
>>> A            C                 G                        T
>>> 1             0                  1                        4
>>> 4             0                  0                        2
>>> 4              2                 0                        0
>>> 1              5                 0                        0
>>> 0              0                 4                        3
>
> It's also possible to apply the logic that Gabor Grothendieck offered
> at the beginning of this thread:
>
> dat[, "newcol"] <- apply(dat, 1, function(x) gsub("\\,|\\." ,x[1],
> x[2])  )
> # ... and the obvious repetition for C.G.T
>
>> dat[,"A"] <- nchar( gsub("[^aA]", "", dat[ , "newcol"] ))
>> dat
>    col3       col9     newcol A
> 1     T     .a,g,,     TaTgTT 1
> 2     A     .t,t,,     AtAtAA 4
> 3     A     .,c,c,     AAcAcA 4
> 4     C     .,a,,,     CCaCCC 1
> 5     G    .,t,t,t    GGtGtGt 0
> 6     A  .c,,g,^!.  AcAAgA^!A 5
> 7     A .g,ggg.^!, AgAgggA^!A 4
> 8     A  .$,,,,,.,  A$AAAAAAA 8
> 9     C    a,g,,t,    aCgCCtC 1
> 10    T ,,,,,.,^!. TTTTTTT^!T 0
> 11    T ,$,,,,.,." T$TTTTTTT" 0
>
> I am deeply in debt to Gabor Grothendieck. He taught me all I know
> regarding regex. The man is a master at patterns.
>
> --
>
> David Winsemius, MD
> West Hartford, CT
>

David Winsemius, MD
West Hartford, CT