[adegenet-forum] creating genlight object from 48K SNP data file

[Jombart, Thibaut]

Hello Linda, 

actually, this should not be an error but merely a warning. To disable it, use:
###
x <- new("genlight", dat, multicore=FALSE)
###

but this is really cosmetic. Information on the multicore package can be found on CRAN:
http://cran.r-project.org/web/packages/multicore/index.html

It seems to work on MacOS X. Are you really using R 1.4? This version must be outdated by a few centuries: we're now at R 2.13.1. I would be surprised to see the latest version of adegenet working in R1.4 - or anything beside a t-test. You should definitely use the current version, and give "install.packages("multicore") a try. 

All the best

Thibaut.


________________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Linda Rutledge [lrutledge at trentu.ca]
Sent: 13 September 2011 22:16
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] creating genlight object from 48K SNP data file

Hi,

I have been going through the adegenet-genomics tutorial but when I enter the commands:

> dat <- list(toto=c(1,1,0,0), titi=c(NA,1,1,0), tata=c(NA,0,3, NA))
> x <- new("genlight", dat)

I get the error message:

Loading required package: multicore
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'multicore'

I can't find any information about multicore package nor nothing on the archive.

Eventually I want to do a PCA on 48K SNPs of 1100 individuals that is coded as individuals in rows and each SNP column labelled with chromosome location. Coding is integers -1, 0, 1, 2. (example of first 4 snps shown below).

chr1.100091560 chr1.100112448 chr1.100116609 chr1.100127203
1              0              2              0              2
2              2              1              1              1
3              0              2              0              2
4              0              1              1              2
5              0             -1              1              2

I run Mac OX 10.6.8 and R1.4.0

Hope someone out there can help. Thanks.

Linda
_______________________________________________
adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum