Dear all:
I have a list like that,which is a standard str_locate_all() function
(stringr package) output:
$K
start end
$GSEGTCSCSSK
start end
[1,] 6 6
[2,] 8 8
$GFSTTCPAHVDDLTPEQVLDGDVNELMDVVLHHVPEAK
start end
[1,] 6 6
$LVECIGQELIFLLPNK
start end
[1,] 4
dx) find_overlapped_gene(idx,
all_genes_gr)))
However, for 100 genes, it use nearly ~8s by system.time().That means if I
had 5 genes, nearly one hour for just find overlapped gene.
I am just wondering any algorithm or strategy to do that efficiently,
perhaps 5 genes in ~1
ad it in one time?
I think the core problem is that I can't create different objects'
name in the use of loop or sapply() ,but there may be a better way to
do what I want.
Thanks a lot
Yao He
Yao He
--
—
Master candidate in 2rd year
Department
eport raw result.
Can anybody give me some pieces of advice?
Yao He
—
Master candidate in 2rd year
Department of Animal genetics & breeding
Room 436,College of Animial Science&Technology,
China Agriculture University,Beijing,100193
E-mail: yao.h.1
print(O2[2])
print(t.test(a[O2[1],,i],a[O2[2],,i],na.rm=T))
}
I don't think it is an elegant way and I am inexperience to report raw result.
Could you give me more help?
Yao He
2013/1/7 arun :
> Hi,
> You didn't provide any example data. So, I am not sure whether this helps.
&
, is that generate a
high-dimension array a good way ?
Thank you!
Yao He
2013/1/7 arun :
> HI,
> I tried to create an example dataset (as you didn't provide the data).
> set.seed(25)
> a<-array(sample(1:50,60,replace=TRUE),dim=c(2,10,3))
> dimnames(a)[[1]]<-c("1
",row.names(res1))])
> res1
> # meanp.value
> #EMW.13% 14.35000 0.09355374
> #EMW.21% 17.68000 0.09355374
> #EW.17.5.13% 42.87000 0.17464018
> #EW.17.5.21% 45.97333 0.17464018
> #EW.INCU.13% 49.61333 0.43689727
> #EW.INCU.21% 47.08333 0.43689727
>
> A.K.
&g
4018 -9.265622 3.058955
> #EW.INCU 49.61333 47.08333 0.43689727 -7.119234 12.179234
> A.K.
>
>
>
>
> - Original Message -
> From: Yao He
> To: arun
> Cc: R help
> Sent: Monday, January 7, 2013 10:57 AM
> Subject: Re: [R] how to aggregate T-test result in an e
Hi,this is a question about how to set the scale,try this
add a scale_x_discrete() like that:
plot <- tmpplot + geom_line()+scale_x_continuous(breaks=ii)
Yao He
2013/1/8 Francesco Sarracino :
> Dear R helpers,
>
> I am currently having hard time fixing the values on the x-ax
", "GG"), X2476 = c("AA",
> "TT", "TT", "CC", "TT", "CC", "CC", "TT", "CC", "GG", "GG",
> "GG", "GG", "GT", "TC"
Thanks a lot.
The problem is that I don't know how to handle the output list as I
want calculate the frequency of A or G or T or C by row.
Yao He
2013/1/10 Jessica Streicher :
> Sorry, you wanted rows, i wrote for columns
>
> #rows would be:
> test2<-apply(test[,-c(1:4)],1,f
Original Message-
>> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
>> Behalf
>> Of Yao He
>> Sent: Wednesday, January 09, 2013 4:04 PM
>> To: jim holtman
>> Cc: R help
>> Subject: Re: [R] how to count "A", "C&
3.167
> head(res1,3)
>
> # AA AG CC CT GA GG GT TC TG TT
> # 1 29 10 0 0 13 1 0 0 0 0
> # 10 0 4 0 0 6 43 0 0 0 0
> # 100 19 15 0 0 15 4 0 0 0 0
> head(res2,3)
> # id AA AG CC CT GA GG GT TC TG TT
> #1 1 29 10 0 0 13 1 0 0 0 0
0
> 2611 2611 0
> ", header = TRUE)
>
> mat1 <- matrix(nrow = 53, ncol = 53) # initialize with NA's
> mat1[upper.tri(mat1, diag = TRUE)] <- dat$value
>
> mat2 <- matrix(0, nrow = 53, ncol = 53) # initialize with zeros
> mat2[upper.tri(mat2, diag = TRUE)] &
49401
292 38954 49396 4939749398 49399
291 39003 49392
library (plyr) and library (reshape2) and other good packages are OK for me.
Thanks a lot!
Yao He
—
Master candidate in 2rd year
Department of Animal genetics & breeding
of pairs of A, C, G, T, then two pairs e.g., 'AA' 'CT'
>> could be encoded as a single byte
>>
>> alf <- c("A", "C", "G", "T")
>> nms <- outer(alf, alf, paste0)
>> map <- outer(setNames(as.r
xed effect estimates
As asreml-R is not free ,is there any packages for my study?
I heard nlme or lme4 but I'm not sure whether they could incorporate
covariates and what about their computational efficiency?
Thanks for you recommendation
Yao He
—
Master candid
xed effect estimates
As asreml-R is not free ,is there any packages for my study?
I heard nlme or lme4 but I'm not sure whether they could incorporate
covariates and what about their computational efficiency?
Thanks for you recommendation
Yao He
—
Master candid
es(x=factor(FID),y=..count..,fill=STATUS))
But how could I exclude "nosperm" or other levels just in the use of
ggplot2 without generating another dataframe
Thanks a lot
Yao He
Master candidate in 2rd year
Department of Animal genetics & breeding
Room 4
,1],mean)
But I couldn't set the agrument na.rm=T in the mean() function,so the
results are all NAs
Please tell me how to handle NA values in the use of aggregate()
Thanks a lot
Yao He
—
Master candidate in 2rd year
Department of Animal genetics & breeding
Room 436,C
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