R help - Aug 2010 - Extract values from data frame in R

Using R, I would like to find out which Samples (S1, S2, S3, S4, S5) fulfill
the following criteria:contain minimally one value (x, y or z) bigger than
4. Any ideas? Thanks, Alex.
> data
  Sample       x        y      z
1        S1   -0.3    5.3    2.5
2        S2    0.4    0.2   -1.2
3        S3    1.2   -0.6    3.2
4        S4    4.3    0.7    5.7
5        S5    2.4    4.3    2.3

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On 08/09/2010 01:16 AM, Alexander Eggel wrote:
> Using R, I would like to find out which Samples (S1, S2, S3, S4, S5)
fulfill
> the following criteria:contain minimally one value (x, y or z) bigger than
> 4. Any ideas? Thanks, Alex.
>
>> data
>    Sample       x        y      z
> 1        S1   -0.3    5.3    2.5
> 2        S2    0.4    0.2   -1.2
> 3        S3    1.2   -0.6    3.2
> 4        S4    4.3    0.7    5.7
> 5        S5    2.4    4.3    2.3
Untested:

Sample[apply(Sample[-1], 1, function(x) any(x) > 4)), "Sample"]

On Aug 9, 2010, at 2:16 AM, Alexander Eggel wrote:
> Using R, I would like to find out which Samples (S1, S2, S3, S4, S5)  
> fulfill
> the following criteria:contain minimally one value (x, y or z)  
> bigger than
> 4. Any ideas? Thanks, Alex.
>
>> data
>  Sample       x        y      z
> 1        S1   -0.3    5.3    2.5
> 2        S2    0.4    0.2   -1.2
> 3        S3    1.2   -0.6    3.2
> 4        S4    4.3    0.7    5.7
> 5        S5    2.4    4.3    2.3
>
data$Sample[apply(data[, -1], 1, function(xyz) any(xyz > 4))]
[1] "S1" "S4" "S5"


David Winsemius, MD
West Hartford, CT

> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Erik Iverson
> Sent: Sunday, August 08, 2010 11:27 PM
> To: Alexander Eggel
> Cc: r-help at r-project.org
> Subject: Re: [R] Extract values from data frame in R
> 
> On 08/09/2010 01:16 AM, Alexander Eggel wrote:
> > Using R, I would like to find out which Samples (S1, S2, 
> S3, S4, S5) fulfill
> > the following criteria:contain minimally one value (x, y or 
> z) bigger than
> > 4. Any ideas? Thanks, Alex.
> >
> >> data
> >    Sample       x        y      z
> > 1        S1   -0.3    5.3    2.5
> > 2        S2    0.4    0.2   -1.2
> > 3        S3    1.2   -0.6    3.2
> > 4        S4    4.3    0.7    5.7
> > 5        S5    2.4    4.3    2.3
> 
> Untested:
> 
> Sample[apply(Sample[-1], 1, function(x) any(x) > 4)),
"Sample"]
The any(x)>4 should be any(x>4), as in:
  > f1 <- function(data) data[apply(data[-1], 1, function(x) any(x >
4)), "Sample"]
Note that operating a column at a time on a
data is often faster than operating a row at
a time.  E.g.,
  > f2 <- function(data) with(data, Sample[x>4 | y>4 | z>4])
  > makeData <- function (nrow, seed){
      if (!missing(seed)) 
          set.seed(seed)
      data.frame(Sample = sample(paste("S", 1:5, sep = ""),
replace TRUE,
          size = nrow), x = rgamma(nrow, 4), y = rgamma(nrow, 5), 
          z = rgamma(nrow, 3))
    }
  > z <- makeData(10000, seed=73)
  > system.time(v1 <- f1(z))
     user  system elapsed 
     0.27    0.00    0.25 
  > system.time(v2 <- f2(z))
     user  system elapsed 
     0.00    0.01    0.01 
  > identical(v1, v2)
  [1] TRUE
  > length(v1)
  [1] 8390

(I prefer that non-apply approach because apply often
causes trouble when used with data.frames -- it is only
safe when all columns are numeric.)

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com  
> 
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