SOLVED: how to change SnpMatrix in to numeric

Question

[zwang10]

I use read.plink from package snpStats. I use following to read bed file, and I want to get the 0,1,2 matrix.

GENOTYPE=read.plink("chr22_1",na.strings = "NA")

Then, from the manuals, I know there is a "genotypes" value of GNEOTYPE, which is an object of class "SnpMatrix". And I got this

> genotype$genotypes
A SnpMatrix with  1497 rows and  6 columns
Row names:  ALS5085249 ... ALS5227466 
Col names:  rs62224609 ... rs62224618

Can someone tell me how to change it into 0,1,2 matrix?

My work, I tried to use

    coerce(genotype$genotypes,to="numeric")

And I got something like this, which is not numeric.

           rs62224609 rs80167676 rs3013006 rs9604721 rs117246541 rs62224618
ALS5085249 "B/B"      "B/B"      "B/B"     "B/B"     "B/B"       "B/B"     
ALS5085250 "B/B"      "B/B"      "A/B"     "B/B"     "B/B"       "B/B"     
ALS5085251 "A/B"      "A/B"      "B/B"     "B/B"     "A/B"       "A/B"     
ALS5085252 "B/B"      "B/B"      "A/B"     "B/B"     "B/B"       "B/B"     
ALS5085253 "B/B"      "B/B"      "B/B"     "B/B"     "B/B"       "B/B"     
ALS5085254 "A/B"      "B/B"      "A/B"     "B/B"     "B/B"       "A/B"     
Warning message:
In coerce(genotype$genotypes, to = "numeric") :
  direct use of coerce() is deprecated:  use as(from, class(to)) instead

[russhh]

If this is solved, could you post your solution please

Answer 1

[catherinem.ross]

Use the function indicated in the warning message:

as(genotype$genotypes, to="numeric")

the coerce function is deprecated.