R help - Oct 2010 - Comparison of two files with multiple arguments

Hello,

I have an example file which can be generated using:

dat <- read.table(tc <- textConnection(
'T T,G G T
C NA G G
A,T A A NA'), sep="") 

I also have a reference file with the same number of rows, for example:
G
C
A

I would like to transform the file to numerical values using the following
arguments:
1) Where data points have two letters separated by a comma, e.g.
"T,G",
replace with a "2"
2) Where single letter data points match the data point in the corresponding
row of the reference file, replace with a "0"
3) Where single letter data points do not match the reference file, replace
with a "1"
4) NA is left as NA

In the example, the output file would look like:

1 2 0 1
0 NA 1 1
2 0 0 NA

Any advice very much appreciated. Also, if you know of any good books or
online courses that can help me to learn how to deal with these sorts of
data handling queries, that is also great!

Thank you

-- 
View this message in context:
http://r.789695.n4.nabble.com/Comparison-of-two-files-with-multiple-arguments-tp2991043p2991043.html
Sent from the R help mailing list archive at Nabble.com.

Hello,

Here's one way to do it. It assumes dat has character values, not factors.

dat2 <- matrix(0, nrow(dat), ncol(dat))
dat2[ is.na(dat) ] <- NA
dat2[ apply(dat, 2, function(x) grepl(",", x)) ] <- 2
dat2[ apply(dat, 2, function(x) x != ref) ] <- 1

Michael


On 12 October 2010 13:24, burgundy <sauburn at yahoo.com>
wrote:
>
> Hello,
>
> I have an example file which can be generated using:
>
> dat <- read.table(tc <- textConnection(
> 'T T,G G T
> C NA G G
> A,T A A NA'), sep="")
>
> I also have a reference file with the same number of rows, for example:
> G
> C
> A
>
> I would like to transform the file to numerical values using the following
> arguments:
> 1) Where data points have two letters separated by a comma, e.g.
"T,G",
> replace with a "2"
> 2) Where single letter data points match the data point in the
corresponding
> row of the reference file, replace with a "0"
> 3) Where single letter data points do not match the reference file, replace
> with a "1"
> 4) NA is left as NA
>
> In the example, the output file would look like:
>
> 1 2 0 1
> 0 NA 1 1
> 2 0 0 NA
>
> Any advice very much appreciated. Also, if you know of any good books or
> online courses that can help me to learn how to deal with these sorts of
> data handling queries, that is also great!
>
> Thank you
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/Comparison-of-two-files-with-multiple-arguments-tp2991043p2991043.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>