[Rd] p.adjust; n > length(p) (PR#13519)

[lpagie at xs4all.nl]

Full_Name: Ludo Pagie
Version: 2.8.1
OS: linux
Submission from: (NULL) (194.171.7.39)


p.adjust in stats seems to have a bug in handling n>length(p) for (at least) the
methods 'holm' and 'hochberg'.

For method 'holm' the relevant code:
        i <- 1:n
        o <- order(p)
        ro <- order(o)
        pmin(1, cummax((n - i + 1) * p[o]))[ro]

where p is the supplied vector of pvalues and n is the supplied number of
comparisons. If n>length(p) p.adjust() gives a warning:
Warning message:
In (n - i + 1) * p[o] :
  longer object length is not a multiple of shorter object length

to me it seems that instead of 'i <- 1:n', 'i <- 1:length(p)' is required.
Similar cases seem to be true for 'hochberg' and possibly other methods.

(I tried checking whether this bug has been reported but the website broke on
me. appologies if the bug is known already)

Best, Ludo

Netherlands Cancer Institute
Gene Regulation (B4)
van Steensel Group
Plesmanlaan 121
1066 CX Amsterdam
The Netherlands

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email: lpagie at xs4all.nl