[R] Calculating frequencies of multiple values in 200 colomns

[William Dunlap]

Use table(factor(x, levels=your3values))

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Fri, Nov 10, 2017 at 1:32 AM, Allaisone 1 <allaisone1 at hotmail.com> wrote:

>
>
> Thank you for your effort Bert..,
>
>
> I knew what is the problem now, the values (1,2,3) were only an example.
> The values I have are 0 , 1, 2 . Tabulate () function seem to ignore
> calculating the frequency of 0 values and this is my exact problem as the
> frequency of 0 values should also be calculated for the maf to be
> calculated correctly.
>
> ________________________________
> From: Bert Gunter <bgunter.4567 at gmail.com>
> Sent: 09 November 2017 23:51:35
> To: Allaisone 1; R-help
> Subject: Re: [R] Calculating frequencies of multiple values in 200 colomns
>
> [[elided Hotmail spam]]
>
> "For example, if I have the values : 1 , 2 , 3 in each column, applying
> Tabulate () would calculate the frequency of 1 and 2 without 3"
>
> Huh??
>
> > x <- sample(1:3,10,TRUE)
> > x
>  [1] 1 3 1 1 1 3 2 3 2 1
> > tabulate(x)
> [1] 5 2 3
>
> Cheers,
> Bert
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
> On Thu, Nov 9, 2017 at 3:44 PM, Allaisone 1 <allaisone1 at hotmail.com<
> mailto:allaisone1 at hotmail.com>> wrote:
>
> Thank you so much for your replay
>
>
> Actually, I tried apply() function but struggled with the part of writing
> the appropriate function inside it which calculate the frequency of the 3
> values. Tabulate () function is a good start but the problem is that this
> calculates the frequency of two values only per column which means that
> when I apply maf () function , maf value will be calculated using the
> frequency of these 2 values only without considering the frequency of the
> 3rd value. For example, if I have the values : 1 , 2 , 3 in each column,
> applying Tabulate () would calculate the frequency of 1 and 2 without 3 . I
> need a way to calculate the frequencies of all of the 3 values so the
> calculation of maf will be correct as it will consider all the 3
> frequencies but not only 2 .
>
>
> Regards
>
> Allahisone
>
> ________________________________
> From: Bert Gunter <bgunter.4567 at gmail.com<mailto:bgunter.4567 at gmail.com>>
> Sent: 09 November 2017 20:56:39
> To: Allaisone 1
> Cc: r-help at R-project.org
> Subject: Re: [R] Calculating frequencies of multiple values in 200 colomns
>
> This is not a good way to do things! R has many powerful built in
> functions to do this sort of thing for you. Searching  -- e.g. at
> rseek.org<http://rseek.org> or even a plain old google search -- can help
> you find them. Also, it looks like you need to go through a tutorial or two
> to learn more about R's basic functionality.
>
> In this case, something like (no reproducible example given, so can't
> confirm):
>
> apply(Values, 2, function(x)maf(tabulate(x)))
>
> should be close to what you want .
>
>
> Cheers,
> Bert
>
>
>
>
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
> On Thu, Nov 9, 2017 at 11:44 AM, Allaisone 1 <allaisone1 at hotmail.com<
> mailto:allaisone1 at hotmail.com>> wrote:
>
> Hi All
>
>
> I have a dataset of 200 columns and 1000 rows , there are 3 repeated
> values under each column (7,8,10). I wanted to calculate the frequency of
> each value under each column and then apply the function maf () given that
> the frequency of each value is known. I can do the analysis step by step
> like this :-
>
>
> > Values
>
>
>          A       B       C       ... 200
>
> 1      7       10      7
>
> 2      7       8        7
>
> 3      10     8        7
>
> 4       8      7         10
>
> .
>
> .
>
> .
>
>
>
>
> For column A : I calculate the frequency for the 3 values as follows :
>
>  count7 <- length(which(Values$A == 7))
>
> count8 <- length(which(Values$A == 8))
>
> count10 <- length(which(Values$A == 10))
>
>
> count7 = 2, count8 = 1 , count10= 1.
>
>
> Then, I create a vector  and type the frequencies manually :
>
>
>  Freq<- c( count7=2  ,count8= 1,count10=1)
>
>
> Then I apply the function maf ()  :-
>
> maf(Freq)
>
>
> This gives me the result I need for column A , could you please help me
>
> to perform the analysis for all of the 200 columns at once ?
>
>
> Regards
>
> Allahisone
>
>
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>
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>
>
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>
> ______________________________________________
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>

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