[R] replacing a factor value in a data frame

[Federico Calboli]

Hi All,

I have the following problem, that's driving me mad.

I have a dataframe of factors, from a genetic scan of SNPs. I DO have
NAs in the dataframe, which would look like:

   V4 V5 V6 V7   V8   V9 V10
1  TT GG TT AC   AG   AG  TT
2  AT CC TT AA   AA   AA  TT
3  AT CC TT AC   AA <NA>  TT
4  TT CC TT AA   AA   AA  TT
5  AT CG TT CC   AA   AA  TT
6  TT CC TT AA   AA   AA  TT
7  AT CC TT CC <NA> <NA>  TT
8  TT CC TT AC   AG   AG  TT
9  AT CC TT CC   AG <NA>  TT
10 TT CC TT CC   GG   GG  TT


In the dataframe I have 1 column where one factor has been erroneosly
given alternative readings: CG and GC. 

I want to change the instances of GC to CG and I use the code:

data[data[,30]=="GC", 30] = "CG"

but get the error:
Error in "[<-.data.frame"(`*tmp*`, all[, 30] == "GC", 30
        missing values are not allowed in subscripted as

Any hints?

Cheers,

Federico

-- 
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG

Tel  +44 (0)20 7594 1602     Fax (+44) 020 7594 3193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com