resampling from string when it runs across multiple lines

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try this:

y <- as.matrix(read.table(textConnection(
"A     C     G     T     T     G     C     A     G      C
A     C     G     F     F     F     F     F     F      G
A     C     G     S     S     S     S     S     G      A
A     C     G     T     T     G     C     A     G      G
A     B     B     B     B     B     B     A     G      T"
), stringsAsFactors = FALSE))

ind <- sample(length(y), 20, TRUE)
y[ind]

I hope it helps.

Best,
Dimitris

ps, it would be best that you send that kind of e-mails in R-help not  
R-devel; check http://www.r-project.org/mail.html for more info  
regarding the different R-mailing-lists.

----
Dimitris Rizopoulos
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
      http://www.student.kuleuven.be/~m0390867/dimitris.htm

Quoting Suraaga Kulkarni <suraaga.kulkarni at gmail.com>:
Hi,

I need to resample from a long string, which is written in many lines with
carriage-return marks at the end of each line.  Perhaps because the data
looks like a matrix, using the code: sample(data, 25, replace=T) gives me 25
columns of characters from the data because it is resampling whole columns.
What I would like it to do is to treat the data as a vector that has just
been spread across many lines, and pick single characters from random
positions in randomly chosen lines.

I am reproducing a sample dataset, the command and the output here:

y
     X..1. X..2. X..3. X..4. X..5. X..6. X..7. X..8. X..9. X..10.
[1,]     A     C     G     T     T     G     C     A     G      C
[2,]     A     C     G     F     F     F     F     F      F      G
[3,]     A     C     G    S     S     S     S     S     G      A
[4,]     A     C     G     T     T     G     C     A     G      G
[5,]     A     B     B     B     B     B     B     A     G      T

sample(y, 20, replace=T)
     X..9. X..4. X..2. X..7. X..9..1 X..3. X..3..1 X..9..2 X..9..3 X..4..1
X..3..2 X..8. X..9..4 X..3..3 X..6. X..7..1
[1,]     G     T     C     C       G     G       G       G       G
T       G     A       G       G     G       C
[2,]     F      F    C     F        F     G       G       F       F
F       G     F       F       G      F       F
[3,]     G     S    C     S       G     G       G       G       G
S       G     S       G       G     S       S
[4,]     G     T     C     C       G     G       G       G       G
T       G     A       G       G     G       C
[5,]     G     B     B     B       G     B       B       G       G
B       B     A       G       B     B       B

     X..6..1 X..3..4 X..7..2 X..10.
[1,]       G       G       C      C
[2,]       F       G        F      G
[3,]       S       G       S      A
[4,]       G       G       C      G
[5,]       B       B       B       T

I wanted to try the bootstrap approach (since that's what I am doing -
resampling with replacement) but that requires a "statistic" and I don't
know what sense that makes for character data.

Any help will be greatly appreciated.

Thanks,

S.

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