[R] matching genes to a list of gene groups an built binary data frame

[David Winsemius]

On Oct 20, 2014, at 6:28 AM, Karim Mezhoud wrote:

> Genes <- c("ACACA", "BAX" , "BCL2", "BID", "BAX", "MAPK9")
> 
> and a list of group of genes
> 
> ListGroup <- list(group1=c("ACACA" ,"AHSA1"     ,"AIMP2"    , "AKR1B1",
> "AKT1",      "AKT1S1"), group2=c("ANXA1"  ,   "AR"   ,     "ARID1A" ,
> "ATM"     ,  "BAK1" ,     "BAX"  ), group3=c("BCL2"  ,    "BCL2L1"  ,
> "BCL2L11" ,  "BECN1" ,    "BID"  ,     "BIRC2"))

Desired:

> I would like to built a data frame as:
> 
>                   ACACA   BAX  BCL2  BID  BAX   MAPK9
> group1            1             0        0          0     0           0
> group2            0             1         0          0     1           0
> group3            0              0        1           1     0           0
> 


> sapply(Genes, function(x) as.numeric(sapply(ListGroup, '%in%', x=x) ) )
     ACACA BAX BCL2 BID BAX MAPK9
[1,]     1   0    0   0   0     0
[2,]     0   1    0   0   1     0
[3,]     0   0    1   1   0     0

?'%in%'

The x=x asserts that the x value will be used as the first argument to %in% so ListGroup items will be used as the table arguments. It's a matrix, so as.data.frame would be needed to deliver a dfrm.

-- 
David Winsemius
Alameda, CA, USA