[R] Logical statements and subseting data...

[Neil Shephard]

Hi,

I'm scratching my head as to why I can't use the subset() command to
remove one line of data from a data frame.

There is just one row (out of 45840) that I'd like to remove and it
can be identified using....

> dim(raw.all.clean)
[1] 45840    10
> subset(raw.all.clean, Height.1 == 0 & Height.2 == 0)
      Sample.Name Well       SNP Allele.1 Allele.2 Size.1 Size.2 Height.1
47068      CA0153  O02 rs2106776                       NA     NA        0
      Height.2 Pool
47068        0    3

(Note that the row index of 47068 which is higher than the rows
reported by dim() is simply because I have already removed a number of
rows).

So I want to remove this one instance where Height.1 == 0 & Height.2
== 0.  I'd have thought that a logical expression where Height.1 != 0
& Height.2 != 0 would have achieved this, but it doesn't seem to
correctly drop out this one observation, instead its dropping out far
more observations...

> t <- subset(raw.all.clean, Height.1 != 0 & Height.2 != 0)
> dim(t)
[1] 38150    10

Thus 7690 rows have been removed.  It seems to be that the '&'
operator is being interparated as an 'OR' (|) since...

> dim(subset(raw.all.clean, Height.1 != 0))
[1] 42152    10
> dim(subset(raw.all.clean, Height.2 != 0))
[1] 41837    10

...and...

> dim(raw.all.clean) - dim(subset(raw.all.clean, Height.1 != 0))
[1] 3688    0
> dim(raw.all.clean) - dim(subset(raw.all.clean, Height.2 != 0))
[1] 4003    0

> 3688 + 4003
[1] 7691

(This is one more than the number of rows being removed, but given
that there is one sample where both Height.1 and Height.2 are '0'
thats fine).

I thought I understood how logical expressions are constructed, and
have gone back and read the entries on precedence, but can't work out
why the above is happening?

Whats particularly perplexing (to me) is that the test for exact
equality works, but not for inequality?

I feel like I'm missing something blatantly obvious, but can't work
out what it is.

Cheers,

Neil

-- 
Email - nshephard at gmail.com / n.shephard at sheffield.ac.uk