Re: [R] LDheatmap

[David González]

Yes, I used LDheatmap just a moment... First you need to convert your 
matrix (ej. your geno file) to snp.matrix usin the package "chopsticks", 
web> https://bioconductor.org/packages/release/bioc/html/chopsticks.html.

This package is no in R library. You need use a sourse. Use this code>

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R;)
biocLite("chopsticks")

Then, a example to convert your matrix (geno file) to snp.matrix and use 
LDheatmap function

# Pass LDheatmap a snp.matrix object
set.seed(1)
#make an example matrix of genotypes, coded as 0, 1 2 copies of an index allele
gdat<-matrix(rbinom(n=500,size=2,prob=.5),ncol=5) 
require(chopsticks)
gdat<-as(gdat,"snp.matrix")
library(LDheatmap)
LDheatmap(gdat,genetic.distances=c(0,1000,3000,4000,1))

I hope help you..




El miércoles, 3 de febrero de 2016, 18:08:46 (UTC-6), Val escribió:
>
> Thank you Bert, 
>
> Yes I looked a this one and I was looking for if any one has used it or 
> not 
> before?  My data set is different what they are showing in the paper 
>
>
>
>
>
> On Wed, Feb 3, 2016 at 4:00 PM, Bert Gunter  > wrote: 
>
> > Have you looked here (found immediately by an internet search!)? 
> > 
> > 
> https://cran.r-project.org/web/packages/LDheatmap/vignettes/LDheatmap.pdf 
> > 
> > Cheers, 
> > Bert 
> > 
> > 
> > 
> > Bert Gunter 
> > 
> > "The trouble with having an open mind is that people keep coming along 
> > and sticking things into it." 
> > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) 
> > 
> > 
> > On Wed, Feb 3, 2016 at 1:49 PM, Ashta  
> wrote: 
> > > Hi all, 
> > > 
> > > I am  looking for an R package that calculates  a pair wise LD 
> > > (linkage disequilibrium) I came up with  library(LDheatmap).  has any 
> > > one used this library? I would appreciate if I get a help how to use 
> > > this library for my set of data.. 
> > > 
> > > 
> > > My data set look like 
> > > 
> > > Geno file 
> > > Name1 1 1 2 2 2 2 
> > > Name2 2 2 2 2 2 2 
> > > Name3 2 2 2 2 2 2 
> > > Name4  2 2 2 2 2 2 
> > > Name5 1 1 2 2 2 2 
> > > 
> > > 
> > > NameN  1   1 1 2 2 2 2 
> > > 
> > > 
> > > The other file is map file 
> > > Chromosome, SNP, Location (physical) 
> > > 
> > > 
> > > Thank you in advance 
> > > 
> > > __ 
> > > r-h...@r-project.org  mailing list -- To UNSUBSCRIBE and 
> more, see 
> > > 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-h...@r-project.org  mailing list -- To UNSUBSCRIBE and 
> more, see 
> > 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. 
> > 
>
> [[alternative HTML version deleted]] 
>
> __ 
> r-h...@r-project.org  mailing list -- To UNSUBSCRIBE and 
> more, see 
> 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 -- To UNSUBSCRIBE and more, see
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.

Re: [R] LDheatmap

[Bert Gunter]

Have you looked here (found immediately by an internet search!)?

https://cran.r-project.org/web/packages/LDheatmap/vignettes/LDheatmap.pdf

Cheers,
Bert



Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Wed, Feb 3, 2016 at 1:49 PM, Ashta  wrote:
> Hi all,
>
> I am  looking for an R package that calculates  a pair wise LD
> (linkage disequilibrium) I came up with  library(LDheatmap).  has any
> one used this library? I would appreciate if I get a help how to use
> this library for my set of data..
>
>
> My data set look like
>
> Geno file
> Name1 1 1 2 2 2 2
> Name2 2 2 2 2 2 2
> Name3 2 2 2 2 2 2
> Name4  2 2 2 2 2 2
> Name5 1 1 2 2 2 2
>
>
> NameN  1   1 1 2 2 2 2
>
>
> The other file is map file
> Chromosome, SNP, Location (physical)
>
>
> Thank you in advance
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
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.

Re: [R] LDheatmap

[Val]

Thank you Bert,

Yes I looked a this one and I was looking for if any one has used it or not
before?  My data set is different what they are showing in the paper





On Wed, Feb 3, 2016 at 4:00 PM, Bert Gunter  wrote:

> Have you looked here (found immediately by an internet search!)?
>
> https://cran.r-project.org/web/packages/LDheatmap/vignettes/LDheatmap.pdf
>
> Cheers,
> Bert
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Wed, Feb 3, 2016 at 1:49 PM, Ashta  wrote:
> > Hi all,
> >
> > I am  looking for an R package that calculates  a pair wise LD
> > (linkage disequilibrium) I came up with  library(LDheatmap).  has any
> > one used this library? I would appreciate if I get a help how to use
> > this library for my set of data..
> >
> >
> > My data set look like
> >
> > Geno file
> > Name1 1 1 2 2 2 2
> > Name2 2 2 2 2 2 2
> > Name3 2 2 2 2 2 2
> > Name4  2 2 2 2 2 2
> > Name5 1 1 2 2 2 2
> >
> >
> > NameN  1   1 1 2 2 2 2
> >
> >
> > The other file is map file
> > Chromosome, SNP, Location (physical)
> >
> >
> > Thank you in advance
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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 -- To UNSUBSCRIBE and more, see
> 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.
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.