[R] solution
Hello
I am not sure about your general aim, but from my previous experience on
combination of treatments, it can be more useful to create a matrix or
data.frame, which you can fulfill either with 1s and 0s, or with the values of
treatment, especially if you will need this data later for the analysis.
I can propose a small function, but only for the case of pair selection
treat=function(x,y){
data.frame(Treatment=x[-which(x==y)], Comparator=rep(y,times=length(x)-1))
}
treat(c(t1,t2,t3,t4),t2)
Treatment Comparator
1 t1 t2
2 t3 t2
3 t4 t2
In this case you can define the list of names of treatments ant the comparator
each time you need, and you will get the result as a data frame in the way you
asked.
Good luck
Alex Levitchi
PhD in Genetics,
Bioinformatician at Laboratory of Bioinformatics
CBM, Area Science Park, Trieste, Italy
http://www.cbm.fvg.it/laboratories/bioinformatics_research
scientific researcher,
Center of Molecular Biology,
University of Academy of Sciences of Moldova
www.edu.asm.md
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[R] How can I associate a list of defined names with the dataframes to be downloaded
Hello I am very thankful for the reply from Jim Holtman and David Winsemius, especially for the understandable explanations. it really works. Now I get another problem I cannot figure out. That is the situation: I work in biology. I need to download several files according to an experiment, which can be find out in NCBI GEO, and store them. For this I use GEOquery package and getGEO function. Each experiment (named GSE) contains several Samples (GSM), which names I extract by names(GSMList()). So now I want to make association between the defined names, which represents lowercases names of GSM, having them from names(GSMList()) as class(names(GSMList(gse))) [1] character I wrote something like this lapply=(i=1:length(names(GSMList(gse))), lgsms[i]=getGEO(names(GSMList(gse))[i])) but Error: unexpected ',' or anything else if I try to make it directly by associating a name from the list to correspondent GEO file I get this lgsms[1]=getGEO(names(GSMList(gse))[1]) #lgsms - list of lowercases names from names(GSMList()) File stored at: /tmp/RtmpgnMuHv/GSM296650.soft # so it downloaded the file but didn't make the association with the name so I cannot use it. Error in lgsms[1] = getGEO(names(GSMList(gse))[1]) : incompatible types (from S4 to character) in subassignment type fix Generally, working with GEOquery should be done very careful, as previously I also have some problems regarding the characteristics of data extracted from it and the way to convert them in an affordable way. It is a pity, that authors don't give more explanations on it. So I suppose it is also here. Kind regards Alex Levitchi [[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] How can I rearange my dataframe
Hello
I am recently began to work with R, so I am not so experienced.
But anyway I cannot find a clear way to process my dataframe which is a bigger
one.
It shows similar to this
name=c(A,B,C,B,C,C,C,B,C)
nicknames=c(A1,B1,C1,B2,C2,C3,C4,B3,C5)
value=c(4,5,9,2,7,6,3,6,7)
table=data.frame(cbind(name,nickname,value))
table=data.frame(cbind(name,nicknames,value))
table
name nicknames value
1 A A1 4
2 B B1 5
3 C C1 9
4 B B2 2
5 C C2 7
6 C C3 6
7 C C4 3
8 B B3 6
9 C C5 7
So I have to rearrange it in the next way:
- the first column should contain just unduplicated data, I did this, it is OK
and it will look like
1 A
2 B
3 C
- the second column should contain different 'nicknames' which correspond to
the single A, B or C
name nickname value
1 A A1
2 B B1,B2,B3
3 C C1,C2,C3,C4,C5
-the third one should contain the mean value of the numbers which correspond to
the same A, B or C
1 A A1 mean(4)
2 B B1,B2,B3 mean(5,2,6)
3 C C1,C2,C3,C4,C5 mean(9,7,6,3,7)
I did this using a loop 'for'.
to be clear I created tree dataframes which correspond to each of columns, and
finally will combine them
ulist=which(!duplicated(table$name)) # I extract the list of positions in
which I don't have duplications
name1=data.frame(table$name[ulist]) # I extract the list of unique names
nicknames1=data.frame(row.names(1:length(ulist))) # I create a dataframe of
dimension equal to unique list length
value1=data.frame(row.names(1:length(ulist))) # I create a dataframe of
dimension equal to unique list length
for(i in 1:length(ulist)) {
position=which(as.character(name1[i,1])==table$name)
nicknames1[i,1]=toString(table$nicknames[position])
value1[i,1]=mean(as.numeric(table$value[position]))
}
fin=cbind(name1,nicknames1,value1)
colnames(fin)=c(NAME,NICKNAME,VALUE)
fin
NAME NICKNAME VALUE
1 A A1 3.00
2 B B1, B2, B3 3.33
3 C C1, C2, C3, C4, C5 5.20
it works successfully. But in general I work with dataframes of high dimensions
(tens thousands or more rows).
So my loop works too slow (i.e., a dataframe of 2 rows and 3 columns is
processed in about 10 minutes).
I intend to integrate it into a function, so it is obvious that time will be
even longer.
If someone can advise me any possibility to modify which I have done or to the
way I can do it, please give me a message.
King regards to all guys who develop and maintain R sources for such dummies as
me
Alex Levitchi
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