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How can I make a list using aggregate function?

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sureshraj

How can I make a list using aggregate function?

Hi friends,

I need to generate a list, that should contain the quantile value of one column in a data frame. while I am compiling this one i am facing one bug,, Really I cannot find out that where the problem has occurred? Could any one help me to come out from this bug??

Here is the code,
data <- lapply(comb.data$zFE, function(x) aggregate(x, by=list(comb.data[["sequence"]]), quantile, probs=c(0.5,0.8,0.9), na.rm=T))

And I am facing bug like this,
"Error in aggregate.data.frame(as.data.frame(x), ...) :
arguments must have same length"

Thanks,
Suresh

John Kane

Re: How can I make a list using aggregate function?

data? We really should see some sample data. See ?dput for a way to supply some.

John Kane
Kingston ON Canada

> -----Original Message-----
> From: [hidden email]
> Sent: Thu, 28 Jun 2012 01:58:30 -0700 (PDT)
> To: [hidden email]
> Subject: [R] How can I make a list using aggregate function?
>
> Hi friends,
>
> I need to generate a list, that should contain the quantile value of
> one
> column in a data frame. while I am compiling this one i am facing one
> bug,,
> Really I cannot find out that where the problem has occurred? Could any
> one
> help me to come out from this bug??
>
> Here is the code,
> data <- lapply(comb.data$zFE, function(x) aggregate(x,
> by=list(comb.data[["sequence"]]), quantile, probs=c(0.5,0.8,0.9),
> na.rm=T))
>
> And I am facing bug like this,
> "Error in aggregate.data.frame(as.data.frame(x), ...) :
> arguments must have same length"
>
> Thanks,
> Suresh
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/How-can-I-make-a-list-using-aggregate-function-tp4634714.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] 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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______________________________________________
[hidden email] 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.

sureshraj

Re: How can I make a list using aggregate function?

Hi freind,
My data seems to be like , and data frame name is comb.data
sequence weight rsat. zFEl
1 CTTTTCTTGTT 4.6 0.00058 -7.452 3.237
2 ACTTTGAGGTG 4.1 0.00077 -7.169 3.114
3 GTCTTGAACTC 4.8 0.00055 -7.506 3.260
4 GCTTTGAAGAA 6.6 0.00019 -8.568 3.721
5 GCTTTCAACAT 7.0 0.00014 -8.874 3.854
6 TCCTTGTTCAT 3.5 0.00099 -6.918 3.004

So I need to use aggregate function based on sequence column(by=list(comb.data$sequence) for zFE column and I should need to store those results in lists..so result would be like
[[1]]
CTTTTCTTGTT 2.3758 3.237
[[2]]
ACTTTGAGGTG 1.78977 -5.11768684
[[3]]
GTCTTGAACTC 1.987455 1.260
[[1]]
GCTTTGAAGAA 1.019 0.72541
[[4]]
GCTTTCAACAT 0.0423 3.865754
...so I made a code like this,,but i am facing some bugs as i mentioned before,,could you please help to solve this one??I hope now you understand my query...

the code is
"data <- lapply(comb.data$zFE, function(x) aggregate(x,by=list(comb.data[["sequence"]]), quantile, probs=c(0.5,0.8,0.9), na.rm=T)) "

Thanks,,

Rui Barradas

Re: How can I make a list using aggregate function?

Hello,

Your data is a mess, with more columns than column names.
Use

# 20 to 100
dput(head(comb.data, 30)) # paste the output of this in a post.

Anyway, it seems that what you want is (untested)

aggregate(zFEl~sequence, data=comb.data, quantile, probs=c(0.5,0.8,0.9),
na.rm=T)

Hope this helps,

Rui Barradas

Em 28-06-2012 15:10, sureshraj escreveu:

> Hi freind,
> My data seems to be like , and data frame name is comb.data
> sequence weight rsat. zFEl
> 1 CTTTTCTTGTT 4.6 0.00058 -7.452 3.237
> 2 ACTTTGAGGTG 4.1 0.00077 -7.169 3.114
> 3 GTCTTGAACTC 4.8 0.00055 -7.506 3.260
> 4 GCTTTGAAGAA 6.6 0.00019 -8.568 3.721
> 5 GCTTTCAACAT 7.0 0.00014 -8.874 3.854
> 6 TCCTTGTTCAT 3.5 0.00099 -6.918 3.004
>
> So I need to use aggregate function based on sequence
> column(by=list(comb.data$sequence) for zFE column and I should need to store
> those results in lists..so result would be like
> [[1]]
> CTTTTCTTGTT 2.3758 3.237
> [[2]]
> ACTTTGAGGTG 1.78977 -5.11768684
> [[3]]
> GTCTTGAACTC 1.987455 1.260
> [[1]]
> GCTTTGAAGAA 1.019 0.72541
> [[4]]
> GCTTTCAACAT 0.0423 3.865754
> ...so I made a code like this,,but i am facing some bugs as i mentioned
> before,,could you please help to solve this one??I hope now you understand
> my query...
>
> the code is
> "data <- lapply(comb.data$zFE, function(x)
> aggregate(x,by=list(comb.data[["sequence"]]), quantile,
> probs=c(0.5,0.8,0.9), na.rm=T)) "
>
>
> Thanks,,
>
>
>
> --
> View this message in context: http://r.789695.n4.nabble.com/How-can-I-make-a-list-using-aggregate-function-tp4634714p4634764.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] 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.
>

arun kirshna

Re: How can I make a list using aggregate function?

Hi,

The data is indeed very confusing. It has four column names and five columns. Assuming that zFEI is for fifth column, the fourth column is "Unknown1".

dat2<-read.table(text="
sequence              weight rsat. Unknown1 zFEl
1    CTTTTCTTGTT    4.6 0.00058 -7.452 3.237
2    ACTTTGAGGTG    4.1 0.00077 -7.169 3.114
3    GTCTTGAACTC    4.8 0.00055 -7.506 3.260
4 GCTTTGAAGAA    6.6 0.00019 -8.568 3.721
5    GCTTTCAACAT    7.0 0.00014 -8.874 3.854
6 TCCTTGTTCAT    3.5 0.00099 -6.918 3.004
",sep="",header=TRUE)

dat3<-aggregate(dat2$zFEl,by=list(dat2$sequence),quantile,probs=c(0.5,0.8,0.9))
dat4<-as.matrix(data.frame(dat3[,1],unlist(dat3[,2])))
colnames(dat4)<-NULL

dat5<-lapply(seq_len(nrow(dat4)),function(i) dat4[i,])
> dat5
[[1]]
[1] "ACTTTGAGGTG" "3.114"       "3.114"       "3.114"

[[2]]
[1] "CTTTTCTTGTT" "3.237"       "3.237"       "3.237"

[[3]]
[1] "GCTTTCAACAT" "3.854"       "3.854"       "3.854"

[[4]]
[1] "GCTTTGAAGAA" "3.721"       "3.721"       "3.721"

[[5]]
[1] "GTCTTGAACTC" "3.260"       "3.260"       "3.260"

[[6]]
[1] "TCCTTGTTCAT" "3.004"       "3.004"       "3.004"

The results I guess is fairly closer to the form you want to store as a list.
A.K.

----- Original Message -----
From: Rui Barradas <[hidden email]>
To: sureshraj <[hidden email]>
Cc: [hidden email]
Sent: Thursday, June 28, 2012 12:09 PM
Subject: Re: [R] How can I make a list using aggregate function?

Hello,

Your data is a mess, with more columns than column names.
Use

# 20 to 100
dput(head(comb.data, 30)) # paste the output of this in a post.

Anyway, it seems that what you want is (untested)

aggregate(zFEl~sequence, data=comb.data, quantile, probs=c(0.5,0.8,0.9),
na.rm=T)

Hope this helps,

Rui Barradas

Em 28-06-2012 15:10, sureshraj escreveu:

______________________________________________
[hidden email] 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.

______________________________________________
[hidden email] 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.

Jim Lemon

Re: How can I make a list using aggregate function?

In reply to this post by sureshraj

On 06/28/2012 06:58 PM, sureshraj wrote:

> Hi friends,
>
> I need to generate a list, that should contain the quantile value of one
> column in a data frame. while I am compiling this one i am facing one bug,,
> Really I cannot find out that where the problem has occurred? Could any one
> help me to come out from this bug??
>
> Here is the code,
> data<- lapply(comb.data$zFE, function(x) aggregate(x,
> by=list(comb.data[["sequence"]]), quantile, probs=c(0.5,0.8,0.9), na.rm=T))
>
> And I am facing bug like this,
> "Error in aggregate.data.frame(as.data.frame(x), ...) :
> arguments must have same length"
>

Hi Suresh,
If your code is accurate, you have an element of the data frame
comb.data named zFEl and you are asking for an element named zFE, which
isn't there, and thus has length zero. Is your error simply one of
misspelling?

Jim

______________________________________________
[hidden email] 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.

sureshraj

Re: How can I make a list using aggregate function?

In reply to this post by sureshraj

Ooops!!! Thanks you friends for your valuable comments,

Finally I found the solution for that,,
Neways thanks....