HI,
Assuming that "out_dat.txt" is the output you expected.
dat1<- read.table("data1.txt",header=TRUE,stringsAsFactors=FALSE)
dat2<- read.table("data2.txt",header=TRUE,stringsAsFactors=FALSE)
out_dat<- read.table("out_data.txt",header=TRUE,stringsAsFactors=FALSE)
out_dat2<-merge(dat1[,1:4],dat2,by="ID")
identical(out_dat,out_dat2)
#[1] TRUE
A.K.
________________________________
From: Vivek Das <vd4mm...@gmail.com>
To: arun <smartpink...@yahoo.com>
Cc: R help <r-help@r-project.org>
Sent: Tuesday, May 7, 2013 6:07 PM
Subject: Re: R help for creating expression data of Differentially expressed
genes
HI Arun,
My data sets are as in the provided files. I am providing the sample files. I
guess this will give a better idea to the type of working I want to do with the
two files and the kind or script am trying to write. Hope you can give me some
suggestions regarding this. I am new to R so having trouble to use different
functions to use this for my working.
Anyone who can help me out with this can be of great help.
----------------------------------------------------------
Vivek Das
PhD Student in Computational Biology
Giuseppe Testa's Lab
European School of Molecular Medicine
IFOM-IEO Campus
Via Adamello, 16
Milan, Italy
emails: vivek....@ieo.eu
vchris...@yahoo.co.in
vd4mm...@gmail.com
On Tue, May 7, 2013 at 10:36 PM, arun <smartpink...@yahoo.com> wrote:
Hi Vivek,
>
>May be this helps:
>set.seed(35)
> dat1<- cbind(ID=1:8,
>as.data.frame(matrix(sample(1:50,8*7,replace=TRUE),ncol=7)))
>
>set.seed(38)
>dat2<- cbind(ID= sample(1:20,8,replace=FALSE),
>as.data.frame(matrix(sample(1:50,8*33,replace=TRUE),ncol=33)))
>colnames(dat2)[-1]<-gsub("V","X",colnames(dat2)[-1])
> merge(dat1[,1:2],dat2[,1:31],by="ID")
># ID V1 X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 X14 X15 X16 X17 X18 X19 X20
>#1 1 43 44 4 33 47 29 43 31 15 2 34 42 5 18 22 36 34 44 3 45 9
>#2 3 28 4 18 45 24 5 20 30 16 49 34 33 5 24 49 31 10 45 21 26 20
>#3 6 5 16 1 5 2 26 6 40 16 15 50 26 37 22 25 39 16 24 29 50 42
>#4 7 25 26 39 16 29 5 40 15 27 46 16 38 36 42 8 3 29 7 13 18 38
>#5 8 30 3 41 25 38 24 41 44 23 2 45 33 10 18 20 49 19 23 42 25 5
># X21 X22 X23 X24 X25 X26 X27 X28 X29 X30
>#1 14 27 3 21 6 44 33 42 10 29
>#2 48 13 8 47 18 9 23 9 44 3
>#3 25 14 31 19 14 6 26 13 6 49
>#4 43 28 15 6 9 19 43 21 41 21
>#5 1 27 18 3 42 5 16 39 46 47
>
>A.K.
>
>
>
>----- Original Message -----
>
>From: Vivek Das <vd4mm...@gmail.com>
>To: arun <smartpink...@yahoo.com>
>Cc:
>
>Sent: Tuesday, May 7, 2013 3:45 PM
>Subject: R help for creating expression data of Differentially expressed genes
>
>Hi Arun,
>
>I need some help regarding R scripting. I have two data file one containing
>seven columns and the other containing 33. Both files have unique identifier
>as ID. I want to create another file which should have the first two columns
>of the first file and and the 31 columns of the second file matched on the
>basis of ID. The first file is having gene I'd and gene names of around 500
>and I want the output file which is having all of those and other attributes
>as well. I want to get the output file having all attributes matching with the
>I'd of the first file. So that I get output of 500 rows with all the
>attributes of second file. I am new to R but having trouble with merge
>function in R. If you can help it will be great.
>
>Regards,
>Vivek
>
>Sent from my iPad
>
>On 07/mag/2013, at 21:13, arun <smartpink...@yahoo.com> wrote:
>
>> HI Ye,
>>
>> For the NA in ID column,
>>
>>
>>
>> Hi
>> dat1<- read.table(text="
>> ObsNumber ID Weight
>> 1 0001 12
>> 2 0001 13
>> 3 0001 14
>> 4 0002 16
>> 5 0002 17
>> 6 N/A 18
>> ",sep="",header=TRUE,colClass=c("numeric","character","numeric"),na.strings="N/A")
>> unlist(lapply(split(dat1,dat1$ID),function(x)
>>with(x,as.character(interaction(ID,seq_len(nrow(x)),sep="_")))),use.names=FALSE)
>> #[1] "0001_1" "0001_2" "0001_3" "0002_1" "0002_2"
>> A.K.
>> ________________________________
>> From: Ye Lin <ye...@lbl.gov>
>> To: arun <smartpink...@yahoo.com>
>> Cc: R help <r-help@r-project.org>
>> Sent: Tuesday, May 7, 2013 2:54 PM
>> Subject: Re: [R] create unique ID for each group
>>
>>
>>
>> Thanks A.K. But I have "NA" in ID column, so when I apply the code, it gives
>> me error saying the replacement as less rows than the data has. Anyway for
>> ID=N/A, return sth like "N/A_1" in order as well?
>>
>>
>>
>>
>>
>>
>> On Tue, May 7, 2013 at 11:17 AM, arun <smartpink...@yahoo.com> wrote:
>>
>> H,
>>> Sorry, a mistake:
>>> dat1$UniqueID<-unlist(lapply(split(dat1,dat1$ID),function(x)
>>> with(x,as.character(interaction(ID,seq_len(nrow(x)),sep="_")))),use.names=FALSE)
>>> dat1
>>> # ObsNumber ID Weight UniqueID
>>> #1 1 0001 12 0001_1
>>> #2 2 0001 13 0001_2
>>> #3 3 0001 14 0001_3
>>> #4 4 0002 16 0002_1
>>> #5 5 0002 17 0002_2
>>>
>>> dat2$UniqueID<-unlist(lapply(split(dat2,dat2$ID),function(x)
>>> with(x,as.character(interaction(ID,seq_len(nrow(x)),sep="_")))),use.names=FALSE)
>>>
>>> A.K.
>>>
>>>
>>>
>>>
>>>
>>> ----- Original Message -----
>>>
>>> From: arun <smartpink...@yahoo.com>
>>> To: Ye Lin <ye...@lbl.gov>
>>> Cc: R help <r-help@r-project.org>
>>> Sent: Tuesday, May 7, 2013 2:10 PM
>>> Subject: Re: [R] create unique ID for each group
>>>
>>>
>>>
>>> Hi,
>>>
>>> Try this:
>>> dat1<- read.table(text="
>>> ObsNumber ID Weight
>>> 1 0001 12
>>> 2 0001 13
>>> 3 0001 14
>>> 4 0002 16
>>> 5 0002 17
>>> ",sep="",header=TRUE,colClass=c("numeric","character","numeric"))
>>> dat2<- read.table(text="
>>> ID Height
>>> 0001 3.2
>>> 0001 2.6
>>> 0001 3.2
>>> 0002 2.2
>>> 0002 2.6
>>> ",sep="",header=TRUE,colClass=c("character","numeric"))
>>> dat1$UniqueID<-with(dat1,as.character(interaction(ID,ObsNumber,sep="_")))
>>>
>>>dat2$UniqueID<-with(dat2,as.character(interaction(ID,rownames(dat2),sep="_")))
>>> dat2
>>> # ID Height UniqueID
>>> #1 0001 3.2 0001_1
>>> #2 0001 2.6 0001_2
>>> #3 0001 3.2 0001_3
>>> #4 0002 2.2 0002_4
>>> #5 0002 2.6 0002_5
>>> A.K.
>>>
>>>
>>>
>>> ----- Original Message -----
>>> From: Ye Lin <ye...@lbl.gov>
>>> To: R help <r-help@r-project.org>
>>> Cc:
>>> Sent: Tuesday, May 7, 2013 1:54 PM
>>> Subject: [R] create unique ID for each group
>>>
>>> Hey All,
>>>
>>> I have a dataset(dat1) like this:
>>>
>>> ObsNumber ID Weight
>>> 1 0001 12
>>> 2 0001 13
>>> 3 0001 14
>>> 4 0002 16
>>> 5 0002 17
>>>
>>> And another dataset(dat2) like this:
>>>
>>> ID Height
>>> 0001 3.2
>>> 0001 2.6
>>> 0001 3.2
>>> 0002 2.2
>>> 0002 2.6
>>>
>>> I want to merge dat1 and dat2 based on "ID" in order, I know "match" only
>>> returns the first match it finds. So I am thinking create unique ID col in
>>> dat2 and dat2, then merge. But I dont know how to do that so it can be like
>>> this:
>>>
>>> dat1:
>>>
>>> ObsNumber ID Weight UniqueID
>>> 1 0001 12 0001_1
>>> 2 0001 13 0001_2
>>> 3 0001 14 0001_3
>>> 4 0002 16 0002_1
>>> 5 0002 17 0002_1
>>>
>>> dat2:
>>>
>>> ID Height UniqueID
>>> 0001 3.2 0001_1
>>> 0001 2.6 0001_2
>>> 0001 3.2 0001_3
>>> 0002 2.2 0002_1
>>> 0002 2.6 0002_2
>>>
>>> Or if it is possible to merge dat1 and dat2 by matching "ID" but return the
>>> match in order that would be great!
>>>
>>> Thanks for your help!
>>>
>>> [[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.
>>>
>>>
>>
>> ______________________________________________
>> 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.
>
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