[R] replacing a factor value in a data frame

From: Federico Calboli <f.calboli_at_imperial.ac.uk>
Date: Sat 29 Oct 2005 - 01:12:15 EST


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

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Received on Sat Oct 29 02:25:12 2005

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