[R] Calculating frequencies of multiple values in 200 colomns

[Allaisone 1]

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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