Dear users,
i am trying to summarize data using "aggregate" with the following
command:
aggregate(pcr$Ct,c(pcr["Gene"],pcr["Type"],pcr["Rep"]),FUN=function(x){c(mean(x),
sd(x), sd(x)/sqrt(sd(x)))})
and the structure of the resulting data frame is
'data.frame':????66 obs. of??4 variables:
$ Gene: Factor w/ 22 levels "14-3-3e","Act5C",..: 1 2 3 4 5
6 7 8 9 10 ...
$ Type: Factor w/ 2 levels "Std","Unkn": 2 2 2 2 2 2 2 2 2 2
...
$ Rep : int??1 1 1 1 1 1 1 1 1 1 ...
$ x?? : num [1:66, 1:3] 16.3 16.7 18.2 17.1 18.6 ...
The actual data is "bundled" in a matrix $x of the data frame. I would
like to have the columns of this matrix as individual numeric columns in the
same data frame instead of a matrix, but cant really figure it out how to do
this in an efficient way. Could someone help me with the construction of this?
Thanks a lot,
Cyrus
Hi Cyrus,
Try this:
pcr<-data.frame(Ct=runif(66,10,20),Gene=rep(LETTERS[1:22],3),
Type=rep(c("Std","Unkn"),33),Rep=rep(1:3,each=22))
testagg<-aggregate(pcr$Ct,c(pcr["Gene"],pcr["Type"],pcr["Rep"]),
FUN=function(x){c(mean(x), sd(x), sd(x)/sqrt(sd(x)))})
nxcol<-dim(testagg$x)[2]
newxs<-paste("x",1:nxcol,sep="")
for(col in 1:nxcol)
testagg[[newxs[col]]]<-testagg$x[,col]
testagg$x<-NULL
Jim
On Thu, Mar 28, 2019 at 12:39 PM cir p via R-help <r-help at
r-project.org> wrote:>
> Dear users,
> i am trying to summarize data using "aggregate" with the
following command:
>
>
aggregate(pcr$Ct,c(pcr["Gene"],pcr["Type"],pcr["Rep"]),FUN=function(x){c(mean(x),
sd(x), sd(x)/sqrt(sd(x)))})
>
> and the structure of the resulting data frame is
>
> 'data.frame': 66 obs. of 4 variables:
> $ Gene: Factor w/ 22 levels "14-3-3e","Act5C",..: 1 2 3
4 5 6 7 8 9 10 ...
> $ Type: Factor w/ 2 levels "Std","Unkn": 2 2 2 2 2 2 2
2 2 2 ...
> $ Rep : int 1 1 1 1 1 1 1 1 1 1 ...
> $ x : num [1:66, 1:3] 16.3 16.7 18.2 17.1 18.6 ...
>
> The actual data is "bundled" in a matrix $x of the data frame. I
would like to have the columns of this matrix as individual numeric columns in
the same data frame instead of a matrix, but cant really figure it out how to do
this in an efficient way. Could someone help me with the construction of this?
>
> Thanks a lot,
>
> Cyrus
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
You can also use 'dplyr'
library(tidyverse)
result <- pcr %>%
group_by(Gene, Type, Rep) %>%
summarise(mean = mean(Ct),
sd = sd(Ct),
oth = sd(Ct) / sqrt(sd(Ct))
)
Jim Holtman
*Data Munger Guru*
*What is the problem that you are trying to solve?Tell me what you want to
do, not how you want to do it.*
On Wed, Mar 27, 2019 at 7:40 PM Jim Lemon <drjimlemon at gmail.com> wrote:
> Hi Cyrus,
> Try this:
>
> pcr<-data.frame(Ct=runif(66,10,20),Gene=rep(LETTERS[1:22],3),
> Type=rep(c("Std","Unkn"),33),Rep=rep(1:3,each=22))
>
testagg<-aggregate(pcr$Ct,c(pcr["Gene"],pcr["Type"],pcr["Rep"]),
> FUN=function(x){c(mean(x), sd(x), sd(x)/sqrt(sd(x)))})
> nxcol<-dim(testagg$x)[2]
> newxs<-paste("x",1:nxcol,sep="")
> for(col in 1:nxcol)
> testagg[[newxs[col]]]<-testagg$x[,col]
> testagg$x<-NULL
>
> Jim
>
> On Thu, Mar 28, 2019 at 12:39 PM cir p via R-help <r-help at
r-project.org>
> wrote:
> >
> > Dear users,
> > i am trying to summarize data using "aggregate" with the
following
> command:
> >
> >
>
aggregate(pcr$Ct,c(pcr["Gene"],pcr["Type"],pcr["Rep"]),FUN=function(x){c(mean(x),
> sd(x), sd(x)/sqrt(sd(x)))})
> >
> > and the structure of the resulting data frame is
> >
> > 'data.frame': 66 obs. of 4 variables:
> > $ Gene: Factor w/ 22 levels "14-3-3e","Act5C",..:
1 2 3 4 5 6 7 8 9 10
> ...
> > $ Type: Factor w/ 2 levels "Std","Unkn": 2 2 2 2 2
2 2 2 2 2 ...
> > $ Rep : int 1 1 1 1 1 1 1 1 1 1 ...
> > $ x : num [1:66, 1:3] 16.3 16.7 18.2 17.1 18.6 ...
> >
> > The actual data is "bundled" in a matrix $x of the data
frame. I would
> like to have the columns of this matrix as individual numeric columns in
> the same data frame instead of a matrix, but cant really figure it out how
> to do this in an efficient way. Could someone help me with the construction
> of this?
> >
> > Thanks a lot,
> >
> > Cyrus
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>
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