Allaisone 1
2017-Nov-09 19:44 UTC
[R] Calculating frequencies of multiple values in 200 colomns
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 :-> ValuesA B C ... 200 1 7 10 7 2 7 8 7 3 10 8 7 4 8 7 10 . . . 1000 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$A == 10)) count7 = 2, count8 = 1 , count10= 1. Then, I create a vector and type the frequencies manually : Freq<- c( count7=2 ,count8= 1,count10=1) Then I apply the function maf () :- maf(Freq) This gives me the result I need for column A , could you please help me to perform the analysis for all of the 200 columns at once ? Regards Allahisone [[alternative HTML version deleted]]
Bert Gunter
2017-Nov-09 20:56 UTC
[R] Calculating frequencies of multiple values in 200 colomns
This is not a good way to do things! R has many powerful built in functions to do this sort of thing for you. Searching -- e.g. at rseek.org or even a plain old google search -- can help you find them. Also, it looks like you need to go through a tutorial or two to learn more about R's basic functionality. In this case, something like (no reproducible example given, so can't confirm): apply(Values, 2, function(x)maf(tabulate(x))) should be close to what you want . Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Thu, Nov 9, 2017 at 11:44 AM, Allaisone 1 <allaisone1 at hotmail.com> wrote:> > Hi All > > > I have a dataset of 200 columns and 1000 rows , there are 3 repeated > values under each column (7,8,10). I wanted to calculate the frequency of > each value under each column and then apply the function maf () given that > the frequency of each value is known. I can do the analysis step by step > like this :- > > > > Values > > > A B C ... 200 > > 1 7 10 7 > > 2 7 8 7 > > 3 10 8 7 > > 4 8 7 10 > > . > > . > > . > > 1000 > > > For column A : I calculate the frequency for the 3 values as follows : > > count7 <- length(which(Values$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 > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. >[[alternative HTML version deleted]]
Bert Gunter
2017-Nov-09 23:51 UTC
[R] Calculating frequencies of multiple values in 200 colomns
Always reply to the list. I am not a free, private consultant! "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> 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> > *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 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> > 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 >> >> . >> >> . >> >> . >> >> 1000 >> >> >> 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 >> >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posti >> ng-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > >[[alternative HTML version deleted]]
Allaisone 1
2017-Nov-10 09:32 UTC
[R] Calculating frequencies of multiple values in 200 colomns
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 :-> ValuesA 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 [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org<mailto:R-help at r-project.org> mailing list -- To UNSUBSCRIBE and more, see 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. [[alternative HTML version deleted]]
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