Hi,
This: sum(data[,1]=="GG") may not work because you have some NA in
your
data. Try this:
sum( data[ , 1 ] == "GG", na.rm = TRUE )
Regards
2009/3/30 David A.G <dasolexa@hotmail.com>
>
> Dear list,
>
> I am trying to evaluate how many elements in a vector equal a certain
> value. The vectors are the columns of a data.frame, read in using
> read.table():
>
> > dim(data)
> [1] 2600 742
> > data[1:5,1:5]
> SNP001 SNP002 SNP003 SNP004 SNP005
> 1 GG AA TT TT GG
> 2 GG AA TC TT GG
> 3 GG AC CC TT GG
> 4 AG AA TT TT GG
> 5 GG AA TC TT GG
>
> > table(data[,1])
>
> AA AG GG
> 251 1093 1252
>
> but if I do
>
> > sum(data[,1]=="GG")
> [1] NA
>
> I have tried storing the column it in a vector but with same results:
>
> > yyy<-(data[,1])
> > sum(yyy=="GG")
> [1] NA
>
> while if I just get a small number of elements from this vector, it works
> fine
> > yyyy <- yyy[1:10]
> > yyyy
> [1] "GG" "GG" "GG" "AG"
"GG" "GG" "AA" "GG" "AG"
"GG"
> > table(yyyy)
> yyyy
> AA AG GG
> 1 2 7
> > sum(yyyy=="GG")
> [1] 7
>
> I checked the archives for help but couldn´t find my error
> What am I missing?
>
> > sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
>
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> Thanks
>
> Dave
>
>
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