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(0,1000,3000,4000,10000))
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 <bgunte...@gmail.com
> <javascript:>> 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 <sew...@gmail.com <javascript:>>
> 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 <javascript:> 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 <javascript:> 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 <javascript:> 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.
