Re: [R] How to remove some rows from a data.frame

From: affy snp <affysnp_at_gmail.com>
Date: Mon, 24 Dec 2007 11:30:04 -0500

Dear Henrique,

Thanks a lot for the help! I got 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))
Error in split.default(df, paste(df$s1, df$s2)) :   first argument must be a vector

Any clue?

Best,

     Allen

On Dec 24, 2007 11:27 AM, Henrique Dallazuanna <wwwhsd_at_gmail.com> wrote:

> 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 <affysnp_at_gmail.com> 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 <m_olshansky_at_yahoo.com> 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 <affysnp_at_gmail.com> 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_at_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_at_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
>

        [[alternative HTML version deleted]]



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