[R] Help: calculations based on three matrices

[Berend Hasselman]

On 24-09-2013, at 16:51, arun <smartpink111 at yahoo.com> wrote:

> Hi,
> Try:
> ME<- matrix(NA,dim(geno[1]),dim(geno)[2])
> indx0<- geno==0 & !is.na(geno)
> ME[indx0]<- Mx[indx0]+My[indx0]
>  indx1<- geno==1 & !is.na(geno)
> ME[indx1]<- apply(cbind(Mx[indx1],My[indx1]),1,max)
> 
I would do this to avoid the apply

ME[indx1]<- pmax(Mx[indx1],My[indx1]) 

Berend

> ME
> A.K.
> 
> 
> 
> 
> ----- Original Message -----
> From: JiangZhengyu <zhyjiang2006 at hotmail.com>
> To: "r-help at r-project.org" <r-help at r-project.org>
> Cc: 
> Sent: Tuesday, September 24, 2013 10:07 AM
> Subject: [R] Help: calculations based on three matrices
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dear R experts,
> 
> I have 3 matrices - "Mx", "My" and "geno" that have the same exact dimensions (attached).  I want to calculate a expression matrix (ME) of the same dimension as well. It is a little complicated.
> 
> To calculate and for a specific cell in ME,  e.g. ME[2,2],
> 
> if value of geno[2,2] is 0, ME[2,2]=Mx[2,2]+My[2,2];
> if value of geno[2,2] is 1, ME[2,2]=the larger number of Mx[2,2] and My[2,2]
> if value of geno[2,2] is NA, ME[2,2]=NA
> 
> I tried to make codes below, but did not work and got stuck. I was wondering if anyone could help with better coding.
> 
> Thanks in advance,
> Zhengyu
> 
> -----------------------------------------------  
> 
> Mx <-  read.table("Mx.txt",header=TRUE, sep="\t", na.strings="NA", dec=".", strip.white=TRUE)
> My <-  read.table("My.txt",header=TRUE, sep="\t", na.strings="NA", dec=".", strip.white=TRUE)
> geno <-  read.table("geno.txt",header=TRUE, sep="\t", na.strings="NA", dec=".", strip.white=TRUE)
> 
> #Calculate Exp for geno==0
> ind=which(geno==0,arr.ind=T)
> het=Mx+My
> ME=matrix(het,nrow=nrow(geno),ncol=ncol(geno))
> ME[ind]=het[ind]
> 
> #Calculate Exp for geno==1
> ind=which(geno==1,arr.ind=T)
> hom=apply(M1,c(1:2),function(x)max(M1[],M2[]))# error
> ME=matrix(hom,nrow=nrow(geno),ncol=ncol(geno))
> ME[ind]=hom[ind]
> 
> # I think the first calculation (geno==0) will be replaced but I don't know how to keep them.
> 
>> head(Mx)
>    X1cX X2cX  X3cX  X4cX X5cX X6cX X7cX X8cX
> 1 26383 6252 14319 16421 2225  480 2038 1164
> 2   636  310   351   341  218  656  412  267
> 3   301  299   752   236  239  309  283  195
> 4  1016 1046  1364   782  822  274  437  346
> 5  1261 1272  1076  1037  659  337 1143 1195
> 6   609  414   393   459  215  429  566  236
> 
>> dim(Mx)
> [1] 20  8
> 
>> head(My)
>    X1cY X2cY X3cY X4cY X5cY X6cY X7cY X8cY
> 1  1039  233  408  607  275 1837 1319  149
> 2  7146 1706 2248 2346 1596  544 2696  417
> 3   266  425 1186  214  325  369  377  215
> 4   260  282  238  240  264  265  317  203
> 5  1070 1052  746  613  384  447  456  683
> 6 13032 1708 2328 5998 2529  923 1068  145
> 
>> dim(My)
> [1] 20  8
> 
>> head(geno)
>   P1 P2 P3 P4 P5 P6 P7 P8
> 1 NA NA NA NA  1 NA NA NA
> 2  1  1  1  1  1  1  1  1
> 3  1  1  0  0  0  0  1  0
> 4  1  1  1  1  1  1  0  0
> 5  0  0  0  0  0  0  1  0
> 6 NA NA NA NA NA NA NA NA
> 
>> dim(geno)
> [1] 20  8
> 
> 
> 
>                                                      
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> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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