[R] If statements for vectors

[Paul Johnson]

On Wed, Apr 9, 2008 at 4:07 PM, Laura Bonnett <L.J.Bonnett at warwick.ac.uk> wrote:
> Dear Sirs,
>
>  I am using both the Bioconductor adds on (Affy, AffyPLM,...) and the
>  'standard' R-package.
>
>  I am trying to select a list of genes which all have expression values below
>  a certain threshold.
>  I have done this by creating a vector which has 0s where the expression is
>  greater than the threshold and 1s where it is less than or equal to it.
>  Multiplying this vector by the expression values produces a list of 0s and
>  expression values below the threshold value.
>
>  However, now I need to remove the 0s.  I thought that this would be
>  relatively trivial but it appears it isn't!!!
>

Without a working example from you, I have no way to test this
proposal.  But if I were you, I would get the index values of the
right cases in one step, and then use that to choose the ones I want.

theGoodOnes <- which(exp2 >= 0)
exp3 <- exp2[theGoodOnes]


This can be crammed into one line, but I'd do it in two just to make
sure it is correct, at least the first time.

My example:

> x <- rnorm(100)
> which(x >= 0)
 [1]  9 11 12 13 14 16 19 20 21 22 24 25 28 30 32 34 35 36 38 40 41 42 43 44 46
[26] 47 49 50 53 54 57 59 61 63 64 66 68 69 70 72 75 78 80 81 82 83 88 90 97 98
> theGoodOnes <- which(x>=0)
> newX <- x[theGoodOnes]
> newX
 [1] 0.89285908 0.51753998 1.18485887 2.10003705 0.54535841 1.28313738
 [7] 1.34092172 0.76064356 0.02201121 0.80808363 0.04578730 0.23045983
[13] 1.04306626 0.12694184 0.89706863 0.86302992 1.53471660 0.51192410
[19] 1.00366834 1.76923470 0.49508470 1.27888454 0.76706729 1.46340483
[25] 1.69315538 0.50537603 0.18422329 0.72968629 0.45490526 2.18208183
[31] 0.71926926 0.68915832 1.49076770 0.48763971 0.39273110 0.80709549
[37] 0.22099019 0.38103757 0.14626929 0.63933750 1.26643194 3.33091910
[43] 2.50341609 2.05286611 0.31986095 0.64548972 0.34712937 0.04075135
[49] 0.07206342 0.20325505


-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas