[R] average duplicated rows?

[arun]

HI,

You can also try this:
dat1<-read.table(text="
            gene_id sample_1 sample_2   FL_EARLY  FL_LATE
763938  Eucgr.A00054   fl_S1E   fl_S1L  13.170800  22.2605
763979  Eucgr.A00101   fl_S1E   fl_S1L   0.367960  14.1202
1273243 Eucgr.A00101    fl_S2   fl_S1L   0.356625  14.1202
764169  Eucgr.A00350   fl_S1E   fl_S1L   7.381070  43.9275
1273433 Eucgr.A00350    fl_S2   fl_S1L  10.674500  43.9275
1273669 Eucgr.A00650    fl_S2   fl_S1L  33.669100  50.0169
764480  Eucgr.A00744   fl_S1E   fl_S1L 132.429000 747.2770
1273744 Eucgr.A00744    fl_S2   fl_S1L 142.659000 747.2770
764595  Eucgr.A00890   fl_S1E   fl_S1L   2.937760  14.9647
764683  Eucgr.A00990   fl_S1E   fl_S1L   8.681250  48.5492
1273947 Eucgr.A00990    fl_S2   fl_S1L  10.553300  48.5492
764710  Eucgr.A01020   fl_S1E   fl_S1L   0.000000  57.9273
1273974 Eucgr.A01020    fl_S2   fl_S1L   0.000000  57.9273
764756  Eucgr.A01073   fl_S1E   fl_S1L   8.504710 101.1870
1274020 Eucgr.A01073    fl_S2   fl_S1L   5.400010 101.1870
764773  Eucgr.A01091   fl_S1E   fl_S1L   3.448910  15.7756
764826  Eucgr.A01152   fl_S1E   fl_S1L  69.565700 198.2320
764831  Eucgr.A01158   fl_S1E   fl_S1L   7.265640  30.9565
764845  Eucgr.A01172   fl_S1E   fl_S1L   3.248020  16.9127
764927  Eucgr.A01269   fl_S1E   fl_S1L  18.710200  76.6918 
",sep="",header=TRUE,stringsAsFactors=FALSE)


do.call(rbind,lapply(lapply(split(dat1,dat1$gene_id),`[`,4:5),colMeans))
                FL_EARLY  FL_LATE
#Eucgr.A00054  13.1708000  22.2605
#Eucgr.A00101   0.3622925  14.1202
#Eucgr.A00350   9.0277850  43.9275
#Eucgr.A00650  33.6691000  50.0169
#Eucgr.A00744 137.5440000 747.2770
#Eucgr.A00890   2.9377600  14.9647
#Eucgr.A00990   9.6172750  48.5492
#Eucgr.A01020   0.0000000  57.9273
#Eucgr.A01073   6.9523600 101.1870
#Eucgr.A01091   3.4489100  15.7756
#Eucgr.A01152  69.5657000 198.2320
#Eucgr.A01158   7.2656400  30.9565
#Eucgr.A01172   3.2480200  16.9127
#Eucgr.A01269  18.7102000  76.6918


In addition to aggregate(), ddply() etc.

library(data.table)
dat2<-data.table(dat1)
dat3<-dat2[,list(FL_EARLY=mean(FL_EARLY),FL_LATE=mean(FL_LATE)),list(gene_id)]
#aggregate()
dat4<-with(dat1,aggregate(cbind(FL_EARLY,FL_LATE),list(gene_id),FUN=mean))
colnames(dat4)<-colnames(dat1)[c(1,4,5)]
#ddply()
library(plyr)
dat5<-ddply(dat1,.(gene_id),colwise(mean,c("FL_EARLY","FL_LATE")))

A.K.

----- Original Message -----
From: "Vining, Kelly" <Kelly.Vining at oregonstate.edu>
To: "r-help at r-project.org" <r-help at r-project.org>
Cc: 
Sent: Friday, October 12, 2012 11:41 AM
Subject: [R] average duplicated rows?

Dear useRs,

I have a slightly complicated data structure and am stuck trying to extract what I need. I'm pasting an example of this data below. In some cases, there are duplicates in the "gene_id" column because there are two different "sample 1" values for a given "sample 2" value. Where these duplicates exist, I need to average the corresponding "FL_EARLY" values and retain the "FL_LATE" value and replace those two rows with a row containing the "FL_EARLY" average so that I no longer have any "gene_id" duplicates.

Seems like this is a job for some version of the apply function, but searching and puzzling over this has not gotten me anywhere. Any help will be much appreciated!

Example data:


             gene_id sample_1 sample_2   FL_EARLY  FL_LATE
763938  Eucgr.A00054   fl_S1E   fl_S1L  13.170800  22.2605
763979  Eucgr.A00101   fl_S1E   fl_S1L   0.367960  14.1202
1273243 Eucgr.A00101    fl_S2   fl_S1L   0.356625  14.1202
764169  Eucgr.A00350   fl_S1E   fl_S1L   7.381070  43.9275
1273433 Eucgr.A00350    fl_S2   fl_S1L  10.674500  43.9275
1273669 Eucgr.A00650    fl_S2   fl_S1L  33.669100  50.0169
764480  Eucgr.A00744   fl_S1E   fl_S1L 132.429000 747.2770
1273744 Eucgr.A00744    fl_S2   fl_S1L 142.659000 747.2770
764595  Eucgr.A00890   fl_S1E   fl_S1L   2.937760  14.9647
764683  Eucgr.A00990   fl_S1E   fl_S1L   8.681250  48.5492
1273947 Eucgr.A00990    fl_S2   fl_S1L  10.553300  48.5492
764710  Eucgr.A01020   fl_S1E   fl_S1L   0.000000  57.9273
1273974 Eucgr.A01020    fl_S2   fl_S1L   0.000000  57.9273
764756  Eucgr.A01073   fl_S1E   fl_S1L   8.504710 101.1870
1274020 Eucgr.A01073    fl_S2   fl_S1L   5.400010 101.1870
764773  Eucgr.A01091   fl_S1E   fl_S1L   3.448910  15.7756
764826  Eucgr.A01152   fl_S1E   fl_S1L  69.565700 198.2320
764831  Eucgr.A01158   fl_S1E   fl_S1L   7.265640  30.9565
764845  Eucgr.A01172   fl_S1E   fl_S1L   3.248020  16.9127
764927  Eucgr.A01269   fl_S1E   fl_S1L  18.710200  76.6918



--Kelly V.


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