Karl Brand
2012-May-07 09:50 UTC
[R] how to deduplicate records, e.g. using melt() and cast()
Esteemed UseRs,
This must be embarrassingly trivial to achieve with e.g., melt() and
cast(): deduplicating records ("pw.X" in example) for a given set of
responses ("cond.Y" in example).
Hopefully the runnable example shows clearly what i have and what i'm
trying to convert it to. But i'm just not getting it, ?cast that is! So
i'd really appreciate some ones patience to clarify this, using the
reshape package, or any other approach.
With sincere thanks in advance,
Karl
## Runnable example
## The data.frame i have:
library("reshape")
my.df <- data.frame(pathway = c(rep("pw.A", 2),
rep("pw.B", 3),
rep("pw.C", 1)),
cond.one = c(0.5, NA, 0.4, NA, NA, NA),
cond.two = c(NA, 0.6, NA, 0.9, NA, 0.2),
cond.three = c(NA, NA, NA, NA, 0.1, NA))
my.df
## The data fram i want:
wanted.df <- data.frame(pathway = c("pw.A", "pw.B",
"pw.C"),
cond.one = c(0.5, 0.4, NA),
cond.two = c(0.6, 0.9, 0.2),
cond.three = c(NA, 0.1, NA))
wanted.df
--
Karl Brand
Dept of Cardiology and Dept of Bioinformatics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 703 2460 |M +31 (0)642 777 268 |F +31 (0)10 704 4161
Petr PIKAL
2012-May-07 10:09 UTC
[R] Odp: how to deduplicate records, e.g. using melt() and cast()
Hi I wold vote aggregate> aggregate(my.df[,-1], list(pathway=my.df$pathway), mean, na.rm=T)pathway cond.one cond.two cond.three 1 pw.A 0.5 0.6 NaN 2 pw.B 0.4 0.9 0.1 3 pw.C NaN 0.2 NaN>Regards Petr> > Esteemed UseRs, > > This must be embarrassingly trivial to achieve with e.g., melt() and > cast(): deduplicating records ("pw.X" in example) for a given set of > responses ("cond.Y" in example). > > Hopefully the runnable example shows clearly what i have and what i'm > trying to convert it to. But i'm just not getting it, ?cast that is! So > i'd really appreciate some ones patience to clarify this, using the > reshape package, or any other approach. > > With sincere thanks in advance, > > Karl > > > ## Runnable example > ## The data.frame i have: > library("reshape") > my.df <- data.frame(pathway = c(rep("pw.A", 2), rep("pw.B", 3), > rep("pw.C", 1)), > cond.one = c(0.5, NA, 0.4, NA, NA, NA), > cond.two = c(NA, 0.6, NA, 0.9, NA, 0.2), > cond.three = c(NA, NA, NA, NA, 0.1, NA)) > my.df > ## The data fram i want: > wanted.df <- data.frame(pathway = c("pw.A", "pw.B", "pw.C"), > cond.one = c(0.5, 0.4, NA), > cond.two = c(0.6, 0.9, 0.2), > cond.three = c(NA, 0.1, NA)) > wanted.df > > > -- > Karl Brand > Dept of Cardiology and Dept of Bioinformatics > Erasmus MC > Dr Molewaterplein 50 > 3015 GE Rotterdam > T +31 (0)10 703 2460 |M +31 (0)642 777 268 |F +31 (0)10 704 4161 > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
Dimitris Rizopoulos
2012-May-07 10:09 UTC
[R] how to deduplicate records, e.g. using melt() and cast()
you could try aggregate(), e.g.,
my.df <- data.frame(pathway = c(rep("pw.A", 2),
rep("pw.B", 3),
rep("pw.C", 1)),
cond.one = c(0.5, NA, 0.4, NA, NA, NA),
cond.two = c(NA, 0.6, NA, 0.9, NA, 0.2),
cond.three = c(NA, NA, NA, NA, 0.1, NA))
aggregate(my.df[-1], my.df['pathway'], sum, na.rm = TRUE)
or
sum. <- function(x) if (all(is.na(x))) NA else sum(x, na.rm = TRUE)
aggregate(my.df[-1], my.df['pathway'], sum.)
I hope it helps.
Best,
Dimitris
On 5/7/2012 11:50 AM, Karl Brand wrote:> Esteemed UseRs,
>
> This must be embarrassingly trivial to achieve with e.g., melt() and
> cast(): deduplicating records ("pw.X" in example) for a given set
of
> responses ("cond.Y" in example).
>
> Hopefully the runnable example shows clearly what i have and what i'm
> trying to convert it to. But i'm just not getting it, ?cast that is! So
> i'd really appreciate some ones patience to clarify this, using the
> reshape package, or any other approach.
>
> With sincere thanks in advance,
>
> Karl
>
>
> ## Runnable example
> ## The data.frame i have:
> library("reshape")
> my.df <- data.frame(pathway = c(rep("pw.A", 2),
rep("pw.B", 3),
> rep("pw.C", 1)),
> cond.one = c(0.5, NA, 0.4, NA, NA, NA),
> cond.two = c(NA, 0.6, NA, 0.9, NA, 0.2),
> cond.three = c(NA, NA, NA, NA, 0.1, NA))
> my.df
> ## The data fram i want:
> wanted.df <- data.frame(pathway = c("pw.A", "pw.B",
"pw.C"),
> cond.one = c(0.5, 0.4, NA),
> cond.two = c(0.6, 0.9, 0.2),
> cond.three = c(NA, 0.1, NA))
> wanted.df
>
>
--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
Web: http://www.erasmusmc.nl/biostatistiek/