search for: maf

...thod subset(), or maybe this is something I don't know about said method that when you're subsetting based on the columns of a data frame you can only use constants (0.1, 2.3, 2.2) instead of variables? Here's a look at my data frame called 'ea.cad.pwr': *>ea.ca.pwr[1:5,] MAF OR POWER 1 0.02 0.01 0.9999 2 0.02 0.02 0.9998 3 0.02 0.03 0.9997 4 0.02 0.04 0.9995 5 0.02 0.05 0.9993* Here's my subset lines which finds no rows: *power1 = subset(ea.cad.pwr, MAF == maf1 & OR == odds) power2 = subset(ea.cad.pwr, MAF == maf2 & OR == odds) * Now when maf1 = 0.2 an...

...k you for the suggestion, Bill. The result is not quite what I would like. Here's sample code for you or anyone else who may be interested: Al1 = c('A','C','C','C') Al2 = c('G','G','G','T') Freq1 = c(0.0078,0.0567,0.9434,0.9908) MAF = c(0.0078,0.0567,0.0566,0.0092) m1 = data.frame(Al1=Al1, Al2=Al2,Freq1=Freq1,MAF=MAF,major_allele='') m1 Al1 Al2 Freq1 MAF major_allele 1 A G 0.0078 0.0078 2 C G 0.0567 0.0567 3 C G 0.9434 0.0566 4 C T 0.9908 0.0092 U...

The loop : AllMAFs <- list() for (i in length(SeparatedGroupsofmealsCombs) { AllMAFs[[i]] <- apply( SeparatedGroupsofmealsCombs[[i]], 2, function(x)maf( tabulate( x+1) )) } gives these errors (I tried this many times and I'm sure I copied it entirely) :- Error in apply(SeparatedGroupsofmealsCombs[[i...

Although the loop seems to be formulated correctly I wonder why it gives me these errors : -object 'i' not found - unexpected '}' in "}" the desired output is expected to be very large as for each dataframe in the list of dataframes I expect to see maf value for each of the 600 columns! and this is only for for one dataframe in the list .. I have around 150-200 dataframes.. not sure how R will store these results.. but first I need the analysis to be done correctly. The final output has to be something like this :- > mafsforeachcolumns(I,II...

...w your code", not=r did you post complete error messages. Both of these practices are strongly recommended by the Posting Guide. Please read it (again?). -- David. > > > the desired output is expected to be very large as for each dataframe in the list of dataframes I expect to see maf value for each of the 600 columns! and this is only for > > for one dataframe in the list .. I have around 150-200 dataframes.. not sure how R will store these results.. but first I need the analysis to be done correctly. The final output has to be something like this :- > > >>...

...gleMealCode,SingleMealCode$MealsCombinations) after investigating the structure of "SeparatedGroupsofmealsCombs" , I can see a list of different databases, each of which represents a different Meal combinations which is great. No, I'm struggling with the last part, how can I run the maf code for all dataframes? when I run this code as before :- maf <- apply(SeparatedGroupsofmealsCombs, 2, function(x)maf(tabulate(x+1))) an error message says : dim(X) must have a positive length . I'm not sure which length I need to specify.. any suggestions to correct this syntax ? Regar...

Hello, All! How might one accomplish this using the by() function? m1 is a data frame. # populate column "m1$major_allele" for ( i in 1:length(m1$major_allele)) { if ( m1$Freq1[i] == m1$MAF[i]){ m1$major_allele[i] = m1$Al1[i] } else{ m1$major_allele[i] = m1$Al2[i] } } Jim [[alternative HTML version deleted]]

Something like the following? AllMAFs <- list() for (i in length(SeparatedGroupsofmealsCombs) { AllMAFs[[i]] <- apply(SeparatedGroupsofmealsCombs[[i]], 2, function(x)maf(tabulate(x+1))) } (untested, of course) Also the solution is a bit generic since I don't know what the output of maf() looks like in your case, and I d...

...2 2 > > 5 44 66 4 1 1 0 1 > > 6 44 66 9 2 0 1 2 > > . > > . > > 600,000 > > > > I wanted to find maf() for each column(from 4 to 600) after calculating the frequency of the 3 values (0,1,2) but this should be done group by group (i.e. group(33-55) : rows 1:3 then group(44-66) :rows 4:6 and so on). > > > I can do the analysis for the entire column but not group by group like this : >...

On 18/11/2017 4:40 PM, Allaisone 1 wrote: > > The loop : > > > AllMAFs <- list() > > for (i in length(SeparatedGroupsofmealsCombs) { > AllMAFs[[i]] <- apply( SeparatedGroupsofmealsCombs[[i]], 2, function(x)maf( tabulate( x+1) )) > } > > > gives these errors (I tried this many times and I'm sure I copied it entirely) :- > &gt...

...... ..$ III : int [1:256] 1 1 2 1 1 2 1 2 1 1 ... ..$ IV : int [1:256] 2 2 2 2 2 2 2 2 2 2 ... any suggestions to solve this issue rather than unlisting the list as this will affect the current shape of data (i.e. being separated dataframes). I need to find maf for each column(I,II,III..600) under this dataframe (33_55) and the rest of dataframes. ________________________________ From: Duncan Murdoch <murdoch.duncan at gmail.com> Sent: 18 November 2017 23:15:15 To: Allaisone 1; David Winsemius Cc: R-help Subject: Re: [R] Complicated analysis for h...

...2 4 44 66 7 0 2 2 2 5 44 66 4 1 1 0 1 6 44 66 9 2 0 1 2 . . 600,000 I wanted to find maf() for each column(from 4 to 600) after calculating the frequency of the 3 values (0,1,2) but this should be done group by group (i.e. group(33-55) : rows 1:3 then group(44-66) :rows 4:6 and so on). I can do the analysis for the entire column but not group by group like this : MAF <- apply(M...

...unction 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 > nee...

...; image plots from the predictors. Is there an easy way to do this? My current (newbie) experience with R would suggest there is but that it's not always easy to find it! f3 <- lm( fc ~ poly( speed, 2 ) + poly( torque, 2 ) + poly( sonl, 2 ) + poly( p_rail, 2 ) + poly( pil_sep, 2 ) + poly( maf, 2 ) + (speed + torque + sonl + p_rail + pil_sep + maf)^2 ) hat <- predict( f3 ) contour( sonl, maf, hat ) Error in contour.default(sonl, maf, hat) : increasing 'x' and 'y' values expected image(sonl, maf, hat) Error in image.default(sonl, maf, hat) : increasing 'x...

...u 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 correct code is: for (i in 1:length(SeparatedGroupsofmealsCombs)) { ... I had mentioned that this is untested, but the error is so obvious ... B. > On Nov 18, 2017, at 4:40 PM, Allaisone 1 <allaisone1 at hotmail.com> wrote: > > > The loop : > > AllMAFs <- list() > > for (i in length(SeparatedGroupsofmealsCombs) { > AllMAFs[[i]] <- apply( SeparatedGroupsofmealsCombs[[i]], 2, function(x)maf( tabulate( x+1) )) > } > > gives these errors (I tried this many times and I'm sure I copied it entirely) :- > Error in ap...

...rt 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 Hotm...

...gt;> >> >> 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...

Greetings, Does anyone know of an R code for classification and regression tree analysis (CART)? Thank you Ron Ron Thornton BVSc, PhD, MACVSc (pathology, epidemiology) Programme Co-ordinator, Active Surveillance Animal Biosecurity MAF Biosecurity Authority P O Box 2526 Wellington, New Zealand phone: 64-4-4744156 027 223 7582 fax: 64-4-474-4133 e-mail: ron.thornton at maf.govt.nz http://www.maf.govt.nz

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...