Re: [R] How to do t.test to rows of a dataframe using apply family function?
Hi
If your function works for you why to bother with apply? If it does not give
you required results, please post some data and show us what is expected.
I would remove unlist from your function and declare list for storing data,
which seems to me more natural for storing results.
t.test.list=function(df,paired){
lll-vector(list, length=nrow(df))
for(i in 1:nrow(df)){
lll[[i]]=t.test(df[i,grp1],df[i,grp2],paired=paired)
}
names(lll)=rownames(df)
lll
}
Regards
Petr
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of my1stbox
Sent: Tuesday, August 26, 2014 3:26 AM
To: R Help
Subject: [R] How to do t.test to rows of a dataframe using apply family
function?
Hi All，
How to do t.test to rows (with two levels, or in other words, groups
of samples) of a dataframe using apply family function? I have done
that using function and loops. And my overall purpose is to calculate
DE genes from two groups of miRNA microarray samples. And I know limma
can do that, but it seems limma doesn't support paired t-test.
t.test.df=function(df,paired){
df.t=c()
for(i in 1:nrow(df)){
df.t=rbind(df.t,unlist(t.test(df[i,grp1],df[i,grp2],paired=paired)))
}
rownames(df.t)=rownames(df)
df.t
}
Bests!
Allen Chiu
2014-08-26
[[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.
Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny
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V případě, že je tento e-mail součástí obchodního jednání:
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- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout;
Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce
s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným
dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost
žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně
pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně
osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi
či osobě jím zastoupené známá.
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Re: [R] How to do t.test to rows of a dataframe using apply family function?
Hi
Please reply also to rhelp, maybe others can offer better answer.
Well, are you aware that by unlist you get all results as character values and
not numbers?
Personally I would use lapply and do.call on final result to get it as data
frame.
Here is example
Some model list data
lll-vector(list,length=2)
lll
[[1]]
NULL
[[2]]
NULL
lll[[1]]-t.test(rnorm(20), rnorm(20))
lll[[2]]-t.test(rnorm(20), rnorm(20))
str(unlist(lll))
Named chr [1:22] 0.0091599930484716 37.9972278626102 ...
- attr(*, names)= chr [1:22] statistic.t parameter.df p.value
conf.int1 ...
do.call(rbind, lapply(lll, rbind))
statistic parameter p.value conf.int estimate null.value alternative
[1,] 0.009159993 37.99723 0.9927394 Numeric,2 Numeric,2 0 two.sided
[2,] 0.1256267 32.93057 0.9007913 Numeric,2 Numeric,2 0 two.sided
methoddata.name
[1,] Welch Two Sample t-test rnorm(20) and rnorm(20)
[2,] Welch Two Sample t-test rnorm(20) and rnorm(20)
Regards
Petr
From: my1stbox [mailto:my1st...@163.com]
Sent: Tuesday, August 26, 2014 10:44 AM
To: PIKAL Petr
Subject: Re: RE: [R] How to do t.test to rows of a dataframe using apply family
function?
Hi Petr，
Thank you! I use unlist() and rbind() because I want the result to be in the
form of a matrix.
Regards
Allen
2014-08-26
发件人：PIKAL Petr petr.pi...@precheza.czmailto:petr.pi...@precheza.cz
发送时间：2014-08-26 14:33
主题：RE: [R] How to do t.test to rows of a dataframe using apply family function?
收件人：my1stboxmy1st...@163.commailto:my1st...@163.com,R
Helpr-help@r-project.orgmailto:r-help@r-project.org
抄送：
Hi
If your function works for you why to bother with apply? If it does not give
you required results, please post some data and show us what is expected.
I would remove unlist from your function and declare list for storing data,
which seems to me more natural for storing results.
t.test.list=function(df,paired){
lll-vector(list, length=nrow(df))
for(i in 1:nrow(df)){
lll[[i]]=t.test(df[i,grp1],df[i,grp2],paired=paired)
}
names(lll)=rownames(df)
lll
}
Regards
Petr
-Original Message-
From: r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org
[mailto:r-help-bounces@r-
project.org] On Behalf Of my1stbox
Sent: Tuesday, August 26, 2014 3:26 AM
To: R Help
Subject: [R] How to do t.test to rows of a dataframe using apply family
function?
Hi All，
How to do t.test to rows (with two levels, or in other words, groups
of samples) of a dataframe using apply family function? I have done
that using function and loops. And my overall purpose is to calculate
DE genes from two groups of miRNA microarray samples. And I know limma
can do that, but it seems limma doesn't support paired t-test.
t.test.df=function(df,paired){
df.t=c()
for(i in 1:nrow(df)){
df.t=rbind(df.t,unlist(t.test(df[i,grp1],df[i,grp2],paired=paired)))
}
rownames(df.t)=rownames(df)
df.t
}
Bests!
Allen Chiu
2014-08-26
[[alternative HTML version deleted]]
__
R-help@r-project.orgmailto: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.
Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny
pouze jeho adresátům.
Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně
jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze
svého systému.
Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email
jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či
zpožděním přenosu e-mailu.
V případě, že je tento e-mail součástí obchodního jednání:
- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a
to z jakéhokoliv důvodu i bez uvedení důvodu.
- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout;
Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce
s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným
dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost
žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně
pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně
osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi
či osobě jím zastoupené známá.
This e-mail and any documents attached to it may be confidential and are
intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender.
Delete the contents of this e-mail
Re: [R] How to do t.test to rows of a dataframe using apply family function?
Thank you so much!
Why do do.call(rbind,lapply(lll,rbind)) and rbind(lapply(lll,rbind)) act so
differently? What is the tricky part of that?
do.call(rbind,lapply(lll,rbind))
statistic parameter p.value conf.int estimate null.value alternative
[1,] 2.775282 37.99977 0.008509272 Numeric,2 Numeric,2 0 two.sided
[2,] -1.498133 37.31294 0.1425116 Numeric,2 Numeric,2 0 two.sided
method data.name
[1,] Welch Two Sample t-test rnorm(20) and rnorm(20)
[2,] Welch Two Sample t-test rnorm(20) and rnorm(20)
rbind(lapply(lll,rbind))
[,1] [,2]
[1,] List,9 List,9
2014-08-26
发件人：PIKAL Petr petr.pi...@precheza.cz
发送时间：2014-08-26 17:58
主题：RE: RE: [R] How to do t.test to rows of a dataframe using apply family
function?
收件人：my1stboxmy1st...@163.com
抄送：R Helpr-help@r-project.org
Hi
Please reply also to rhelp, maybe others can offer better answer.
Well, are you aware that by unlist you get all results as character values and
not numbers?
Personally I would use lapply and do.call on final result to get it as data
frame.
Here is example
Some model list data
lll-vector(list,length=2)
lll
[[1]]
NULL
[[2]]
NULL
lll[[1]]-t.test(rnorm(20), rnorm(20))
lll[[2]]-t.test(rnorm(20), rnorm(20))
str(unlist(lll))
Named chr [1:22] 0.0091599930484716 37.9972278626102 ...
- attr(*, names)= chr [1:22] statistic.t parameter.df p.value
conf.int1 ...
do.call(rbind, lapply(lll, rbind))
statistic parameter p.value conf.int estimate null.value alternative
[1,] 0.009159993 37.99723 0.9927394 Numeric,2 Numeric,2 0 two.sided
[2,] 0.1256267 32.93057 0.9007913 Numeric,2 Numeric,2 0 two.sided
methoddata.name
[1,] Welch Two Sample t-test rnorm(20) and rnorm(20)
[2,] Welch Two Sample t-test rnorm(20) and rnorm(20)
Regards
Petr
From: my1stbox [mailto:my1st...@163.com]
Sent: Tuesday, August 26, 2014 10:44 AM
To: PIKAL Petr
Subject: Re: RE: [R] How to do t.test to rows of a dataframe using apply family
function?
Hi Petr，
Thank you! I use unlist() and rbind() because I want the result to be in the
form of a matrix.
Regards
Allen
2014-08-26
发件人：PIKAL Petr petr.pi...@precheza.cz
发送时间：2014-08-26 14:33
主题：RE: [R] How to do t.test to rows of a dataframe using apply family function?
收件人：my1stboxmy1st...@163.com,R Helpr-help@r-project.org
抄送：
Hi
If your function works for you why to bother with apply? If it does not give
you required results, please post some data and show us what is expected.
I would remove unlist from your function and declare list for storing data,
which seems to me more natural for storing results.
t.test.list=function(df,paired){
lll-vector(list, length=nrow(df))
for(i in 1:nrow(df)){
lll[[i]]=t.test(df[i,grp1],df[i,grp2],paired=paired)
}
names(lll)=rownames(df)
lll
}
Regards
Petr
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of my1stbox
Sent: Tuesday, August 26, 2014 3:26 AM
To: R Help
Subject: [R] How to do t.test to rows of a dataframe using apply family
function?
Hi All，
How to do t.test to rows (with two levels, or in other words, groups
of samples) of a dataframe using apply family function? I have done
that using function and loops. And my overall purpose is to calculate
DE genes from two groups of miRNA microarray samples. And I know limma
can do that, but it seems limma doesn't support paired t-test.
t.test.df=function(df,paired){
df.t=c()
for(i in 1:nrow(df)){
df.t=rbind(df.t,unlist(t.test(df[i,grp1],df[i,grp2],paired=paired)))
}
rownames(df.t)=rownames(df)
df.t
}
Bests!
Allen Chiu
2014-08-26
[[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.
Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny
pouze jeho adresátům.
Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně
jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze
svého systému.
Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email
jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či
zpožděním přenosu e-mailu.
V případě, že je tento e-mail součástí obchodního jednání:
- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a
to z jakéhokoliv důvodu i bez uvedení důvodu.
- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout;
Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce
s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je
Re: [R] How to do t.test to rows of a dataframe using apply family function?
Hi
That is because do.call is one function and rbind another. For both functions
you can find its help page and read:
rbind
vectors or matrices. These can be given as named arguments. Other R objects
will be coerced as appropriate: see sections ‘Details’ and ‘Value’.
The type of a matrix result determined from the highest type of any of the
inputs in the hierarchy raw logical integer double complex character
list .
do.call
what
either a function or a non-empty character string naming the function to be
called.
args
a list of arguments to the function call. The names attribute of args gives the
argument names.
Actually inner lapply was not necessary and simple
do.call(rbind, lll)
gives the same result.
From what I understand from help page, when argument in rbind is list of lists
it returns matrix of lists which are printed as
[,1] [,2]
lll List,9 List,9
do.call takes rbind and uses it on each node of list and this node is coerced
to matrix, which is suitable for changing to data frame.
as.data.frame(do.call(rbind, lll))
It is some magic of R which I use although I do not know much about its
internals. If you are interested, the source code is available.
Regards
Petr
From: my1stbox [mailto:my1st...@163.com]
Sent: Tuesday, August 26, 2014 12:24 PM
To: PIKAL Petr
Cc: R Help
Subject: Re: RE: RE: [R] How to do t.test to rows of a dataframe using apply
family function?
Thank you so much!
Why do do.call(rbind,lapply(lll,rbind)) and rbind(lapply(lll,rbind)) act so
differently? What is the tricky part of that?
do.call(rbind,lapply(lll,rbind))
statistic parameter p.value conf.int estimate null.value alternative
[1,] 2.775282 37.99977 0.008509272 Numeric,2 Numeric,2 0 two.sided
[2,] -1.498133 37.31294 0.1425116 Numeric,2 Numeric,2 0 two.sided
method data.name
[1,] Welch Two Sample t-test rnorm(20) and rnorm(20)
[2,] Welch Two Sample t-test rnorm(20) and rnorm(20)
rbind(lapply(lll,rbind))
[,1] [,2]
[1,] List,9 List,9
2014-08-26
发件人：PIKAL Petr petr.pi...@precheza.czmailto:petr.pi...@precheza.cz
发送时间：2014-08-26 17:58
主题：RE: RE: [R] How to do t.test to rows of a dataframe using apply family
function?
收件人：my1stboxmy1st...@163.commailto:my1st...@163.com
抄送：R Helpr-help@r-project.orgmailto:r-help@r-project.org
Hi
Please reply also to rhelp, maybe others can offer better answer.
Well, are you aware that by unlist you get all results as character values and
not numbers?
Personally I would use lapply and do.call on final result to get it as data
frame.
Here is example
Some model list data
lll-vector(list,length=2)
lll
[[1]]
NULL
[[2]]
NULL
lll[[1]]-t.test(rnorm(20), rnorm(20))
lll[[2]]-t.test(rnorm(20), rnorm(20))
str(unlist(lll))
Named chr [1:22] 0.0091599930484716 37.9972278626102 ...
- attr(*, names)= chr [1:22] statistic.t parameter.df p.value
conf.int1 ...
do.call(rbind, lapply(lll, rbind))
statistic parameter p.value conf.int estimate null.value alternative
[1,] 0.009159993 37.99723 0.9927394 Numeric,2 Numeric,2 0 two.sided
[2,] 0.1256267 32.93057 0.9007913 Numeric,2 Numeric,2 0 two.sided
methoddata.name
[1,] Welch Two Sample t-test rnorm(20) and rnorm(20)
[2,] Welch Two Sample t-test rnorm(20) and rnorm(20)
Regards
Petr
From: my1stbox [mailto:my1st...@163.com]
Sent: Tuesday, August 26, 2014 10:44 AM
To: PIKAL Petr
Subject: Re: RE: [R] How to do t.test to rows of a dataframe using apply family
function?
Hi Petr，
Thank you! I use unlist() and rbind() because I want the result to be in the
form of a matrix.
Regards
Allen
2014-08-26
发件人：PIKAL Petr petr.pi...@precheza.czmailto:petr.pi...@precheza.cz
发送时间：2014-08-26 14:33
主题：RE: [R] How to do t.test to rows of a dataframe using apply family function?
收件人：my1stboxmy1st...@163.commailto:my1st...@163.com,R
Helpr-help@r-project.orgmailto:r-help@r-project.org
抄送：
Hi
If your function works for you why to bother with apply? If it does not give
you required results, please post some data and show us what is expected.
I would remove unlist from your function and declare list for storing data,
which seems to me more natural for storing results.
t.test.list=function(df,paired){
lll-vector(list, length=nrow(df))
for(i in 1:nrow(df)){
lll[[i]]=t.test(df[i,grp1],df[i,grp2],paired=paired)
}
names(lll)=rownames(df)
lll
}
Regards
Petr
-Original Message-
From: r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org
[mailto:r-help-bounces@r-
project.org] On Behalf Of my1stbox
Sent: Tuesday, August 26, 2014 3:26 AM
To: R Help
Subject: [R] How to do t.test to rows of a dataframe using apply family
function?
Hi All，
How to do t.test to rows (with two levels, or in other words, groups
of samples) of a dataframe using apply family function? I have done
that using function and loops. And my overall purpose is to
[R] How to do t.test to rows of a dataframe using apply family function?
Hi All，
How to do t.test to rows (with two levels, or in other words, groups of
samples) of a dataframe using apply family function? I have done that using
function and loops. And my overall purpose is to calculate DE genes from two
groups of miRNA microarray samples. And I know limma can do that, but it seems
limma doesn't support paired t-test.
t.test.df=function(df,paired){
df.t=c()
for(i in 1:nrow(df)){
df.t=rbind(df.t,unlist(t.test(df[i,grp1],df[i,grp2],paired=paired)))
}
rownames(df.t)=rownames(df)
df.t
}
Bests!
Allen Chiu
2014-08-26
[[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.
