Try this:
f <- function(x)
{
cbind.data.frame(chr=unique(x$chr),
Start=min(x$pos),
End=max(x$pos),
Rows=nrow(x),
Pattern=paste("(", x$s1, x$s2, ")")
)
}
do.call("rbind", lapply(lapply(split(df, paste(df$s1, df$s2)), f), unique))
On 24/12/2007, affy snp <[EMAIL PROTECTED]> wrote:
> Thanks Moshe! I apologize for not being so clear about the
> second part. Again, below is how the data looks like. The
> pattern for columns s1 and s2 will be:
>
> (-1 -1) (-1 0) (-1 1) (0 -1) (0 0) (0 1) (1 -1) (1 0) (1 1)
> 104 131 57 631 305 668 33 15 107
>
> There are 9 patterns, in other words, 9 combinations of -1,1, 0
> given in the parenthesis. The occurring numbers are underneath.
> What I wish to have is that: scan the data from the begin,
> if any consecutive rows are of the same pattern (one of the 9
> combinations in the above), we will 'memorize' the following information:
>
> the number in 'chr' column, the number in 'pos' column for the first
> row in the consecutive rows, the number in 'pos' column for the
> last row in the consecutive rows, how many rows of the consecutive
> rows, the corresponding pattern for them.
>
> I forgot to reinforce one requirement before for definition of
> the consecutive rows, which is that they are in the consecutive
> orders and are of the same number of 'chr'.
>
> Just to illustrate this, an example could be that, based on the data:
>
> BAC chr pos s1 s2
> RP11-80G24 1 77465510 0 0
> RP11-198H14 1 78696291 -1 0
> RP11-267M21 1 79681704 -1 0
> RP11-89A19 1 80950808 -1 0
> RP11-6B16 1 82255496 -1 0
> RP11-210E16 2 228801510 -1 0
>
> even though row 2---6 are of the same pattern, which is -1 0
> and are in the consecutive order, but row 6 is of different number
> of 'chr' than other rows. Therefore, we will not count row 6 and
> end up with:
> chr Start End #of_rows pattern
> 1 78696291 82255496 4 (-1 0)
>
> Hope this is clear. Thank you once again and Merry X'mas!
>
> Best,
> Allen
>
>
>
>
>
> > BAC chr pos s1 s2
> > RP11-80G24 1 77465510 -1 0
> > RP11-198H14 1 78696291 -1 0
> > RP11-267M21 1 79681704 -1 0
> > RP11-89A19 1 80950808 -1 0
> > RP11-6B16 1 82255496 -1 0
> > RP11-210E16 1 228801510 0 -1
> > RP11-155C15 1 230957584 0 -1
> > RP11-210F8 1 237932418 0 -1
> > RP11-263L17 2 65724492 0 1
> > RP11-340F16 2 65879898 0 1
> > RP11-68A1 2 67718674 0 0
> > RP11-474G23 2 68318411 0 0
> > RP11-218N6 2 68454651 0 0
> > CTD-2003M22 2 68567494 0 0
> > .....
> >
>
> On Dec 24, 2007 3:54 AM, Moshe Olshansky <[EMAIL PROTECTED]> wrote:
>
> > To answer your firs question try
> >
> > M[-which( M$s1 == 0 & M$s2 == 0),]
> >
> > For the second question, you must start with the more
> > precise definition of the grouping criterion.
> >
> > --- affy snp <[EMAIL PROTECTED]> wrote:
> >
> > > Hello list,
> > >
> > > I have a data frame M like:
> > >
> > > BAC chr pos s1 s2
> > > RP11-80G24 1 77465510 -1 0
> > > RP11-198H14 1 78696291 -1 0
> > > RP11-267M21 1 79681704 -1 0
> > > RP11-89A19 1 80950808 -1 0
> > > RP11-6B16 1 82255496 -1 0
> > > RP11-210E16 1 228801510 0 -1
> > > RP11-155C15 1 230957584 0 -1
> > > RP11-210F8 1 237932418 0 -1
> > > RP11-263L17 2 65724492 0 1
> > > RP11-340F16 2 65879898 0 1
> > > RP11-68A1 2 67718674 0 0
> > > RP11-474G23 2 68318411 0 0
> > > RP11-218N6 2 68454651 0 0
> > > CTD-2003M22 2 68567494 0 0
> > > .....
> > >
> > > how to remove those rows which have 0 for both of
> > > columns s1,s2?
> > > sth like M[!M$21=0&!M$s2=0]?
> > >
> > > Moreover, I want to get a list which could find a
> > > subset of rows which have
> > > the same pattern of data. For example, the first 8
> > > rows in M can be
> > > clustered
> > > into 2 groups (represented below in 2 rows) and
> > > shown as:
> > >
> > > chr Start End # of
> > > rows Pattern
> > > 1 77465510 82255496 5
> > > (-1 0)
> > > 1 228801510 237932418 3
> > > (0 -1)
> > >
> > > Can anybody help me out of this? Thank you very much
> > > and happy holiday!
> > >
> > > Best,
> > > Allen
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-help@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained,
> > > reproducible code.
> > >
> >
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
