# [R] For help in R coding

Bansal, Vikas vikas.bansal at kcl.ac.uk
Sat Jul 2 22:46:32 CEST 2011

```DEAR ALL,
I TRIED THIS CODE AND THIS IS RUNNING PERFECTLY...

txt=df[,9]
dad=data.frame(A = unlist(sapply(gregexpr("A|a", txtvec), function(x) if ( x[[1]] != -1)
length(x) else 0 )),
C = unlist(sapply(gregexpr("C|c", txtvec), function(x) if ( x[[1]] != -1)
length(x) else 0 )),
G = unlist(sapply(gregexpr("G|g", txtvec), function(x) if ( x[[1]] != -1)
length(x) else 0 )),
T = unlist(sapply(gregexpr("T|t", txtvec), function(x) if ( x[[1]] != -1)
length(x) else 0 )),
N = unlist(sapply(gregexpr("\\,|\\.", txtvec), function(x) if ( x[[1]] != -1)
length(x) else 0 )))

Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
________________________________________
From: David Winsemius [dwinsemius at comcast.net]
Sent: Saturday, July 02, 2011 9:04 PM
To: Dennis Murphy
Cc: r-help at r-project.org; Bansal, Vikas
Subject: Re: [R] For help in R coding

On reflection and a bit of testing I think the best approach would be
to use gregexpr. For counting the number of commas, this appears quite
straightforward.

> sapply(gregexpr("\\,", txtvec), function(x) if ( x[[1]] != -1)
length(x) else 0 )
[1] 3 3 3 4 3 3 2 6 4 6 6

It easily generalizes to period and the `|` (or) operation on letters.
( did need to add the check since the length of gregexpr is always at
least one but ihas value -1 when there is no match

> sapply(gregexpr("t|T", txtvec), function(x) if ( x[[1]] != -1)
length(x) else 0 )
[1] 0 2 0 0 3 0 0 0 1 0 0

On Jul 2, 2011, at 3:22 PM, Dennis Murphy wrote:

> Hi:
>
> There seems to be a problem if the string ends in , or . , which makes
> it difficult for strsplit() to pick up if it is splitting on those
> characters. Here is an alternative, splitting on individual characters
>
> charsum <- function(s, char) {
>    u <- strsplit(s, "")
>    sum(sapply(u, function(x) charmatch(x, char)), na.rm = TRUE)
>   }
>
> unname(sapply(txtvec, function(x) charsum(x, ',')))
> unname(sapply(txtvec, function(x) charsum(x, '.')))
>
> Putting this into a data frame,
>
> dfout <- data.frame(periods = unname(sapply(txtvec, function(x)
> charsum(x, '.'))),
>                                commas = unname(sapply(txtvec,
> function(x) charsum(x, '.'))) )
> txtvec
>
> HTH,
> Dennis
>
> On Sat, Jul 2, 2011 at 10:19 AM, David Winsemius <dwinsemius at comcast.net
> > wrote:
>>
>> On Jul 2, 2011, at 12:34 PM, Bansal, Vikas wrote:
>>
>>>
>>>
>>>>> Dear all,
>>>>>
>>>>> I am doing a project on variant calling using R.I am working on
>>>>> pileup file.There are 10 columns in my data frame and I want to
>>>>> count the number of A,C,G and T in each row for column 9.example
>>>>> of
>>>>> column 9 is given below-
>>>>>
>>>>>         .a,g,,
>>>>>         .t,t,,
>>>>>         .,c,c,
>>>>>         .,a,,,
>>>>>         .,t,t,t
>>>>>         .c,,g,^!.
>>>>>         .g,ggg.^!,
>>>>>         .\$,,,,,.,
>>>>>         a,g,,t,
>>>>>         ,,,,,.,^!.
>>>>>         ,\$,,,,.,.
>>>>>
>>>>> This is a bit confusing for me as these characters are in one
>>>>> column
>>>>> and how can we scan them for each row to print number of A,C,G
>>>>> and T
>>>>> for each row.
>>>>
>>>> Seems a bit clunky but this does the job (first the data):
>>>>>
>>>>> txt <- " .a,g,,
>>>>
>>>> +            .t,t,,
>>>> +            .,c,c,
>>>> +            .,a,,,
>>>> +            .,t,t,t
>>>> +            .c,,g,^!.
>>>> +            .g,ggg.^!,
>>>> +            .\$,,,,,.,
>>>> +            a,g,,t,
>>>> +            ,,,,,.,^!.
>>>> +            ,\$,,,,.,."
>>>>
>>>>
>>>> Now the clunky solution, Basically subtracts 1 from the counts of
>>>> "fragments" that result from splitting on each letter in turn.
>>>> Could
>>>> be made prettier with a function that did the job.
>>>>
>>>>> data.frame(A = unlist(lapply( lapply( sapply(txtvec, strsplit,
>>>>
>>>> split="a"), length) , "-", 1)),
>>>> + C = unlist(lapply( lapply( sapply(txtvec, strsplit, split="c"),
>>>> length) , "-", 1)),
>>>> + G = unlist(lapply( lapply( sapply(txtvec, strsplit, split="g"),
>>>> length) , "-", 1)),
>>>> + T = unlist(lapply( lapply( sapply(txtvec, strsplit, split="t"),
>>>> length) , "-", 1)) )
>>>>                     A C G T
>>>> .a,g,,               1 0 1 0
>>>>          .t,t,,     0 0 0 2
>>>>          .,c,c,     0 2 0 0
>>>>          .,a,,,     1 0 0 0
>>>>          .,t,t,t    0 0 0 2
>>>>          .c,,g,^!.  0 1 1 0
>>>>          .g,ggg.^!, 0 0 4 0
>>>>          .\$,,,,,.,  0 0 0 0
>>>>          a,g,,t,    1 0 1 1
>>>>          ,,,,,.,^!. 0 0 0 0
>>>>          ,\$,,,,.,.  0 0 0 0
>>>>
>>>> Has the advantage that the input data ends up as rownames, which
>>>> was a
>>>> surprise.
>>>>
>>>> If you wanted to count "A" and "a" as equivalent, then the split
>>>> argument should be "a|A"
>>>>
>>>>
>>>
>>>>> AS YOU MENTIONED THAT IF I WANT TO COUNT A AND a I SHOULD SPLIT
>>>>> LIKE
>>>>> THIS.
>>>
>>> BUT CAN I COUNT . AND , ALSO USING-
>>> data.frame(A = unlist(lapply( lapply( sapply(txtvec, strsplit,
>>> split=".|,"), length) , "-", 1)),
>>>
>>> I TRIED IT BUT ITS NOT WORKING.IT IS GIVING THE OUTPUT BUT AT SOME
>>> PLACES
>>> IT IS SHOWING MORE NUMBER OF . AND , AND SOMEWHERE IT IS NOT EVEN
>>> CALCULATING AND JUST SHOWING 0.
>>
>> You need to use valid regex expressions for 'split'. Since "." and
>> "," are
>> special characters they need to be escaped when you wnat the
>> literals to be
>> recognized as such.
>>
>> I haven't figured out why but you need to drop the final operation of
>> subtracting 1 from the values when counting commas:
>>
>> data.frame(periods = unlist(lapply( lapply( sapply(txtvec, strsplit,
>>                             split="\\."), length) , "-", 1))
>>  ,commas = unlist( lapply( sapply(txtvec, strsplit,
>>                             split="\\,"), length) ) )
>>                       periods commas
>>  .a,g,,                      1      3
>>            .t,t,,           1      3
>>            .,c,c,           1      3
>>            .,a,,,           1      4
>>            .,t,t,t          1      4
>>            .c,,g,^!.        1      4
>>            .g,ggg.^!,       2      2
>>            .\$,,,,,.,        2      6
>>            a,g,,t,          0      4
>>            ,,,,,.,^!.       1      7
>>            ,\$,,,,.,.        1      7
>>
>> --
>>
>> David Winsemius, MD
>> West Hartford, CT
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help