[adegenet-forum] extract.PLINKmap

[Jombart, Thibaut]

Hello, 

Can you please send a toy dataset and the code to reproduce the error?

Cheers

Thibaut
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of H.Papoli Yazdi [h.papoli.yazdi at student.rug.nl]
Sent: 21 January 2013 15:27
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] extract.PLINKmap

 Hello,

I am encountering a problem in importing my SNP position data for a genlight object in adegenet.

I upload my genlight object using "read.PLINK" function. My .map file has the following format which is the standard PLINK format (chromosome, snp ID, genetic distance and physical position)

1 F0100010 0 7.29827
1 F0100020 0 127.006
1 F0100030 0 11.4989

I used "extract.PLINKmap" function to add the chromosome and position information to my genlight object, but it gives me the error message as follows:

"Warning message:
In matrix (txt, ncol=4, byrow=TRUE):
the length of the data [44706] is not a divisor or multiple of the number of lines [11177]"

Therefore, it does not load the position information. The problem is that it does not transform my .map file into a matrix of 4 columns and 44706 rows but it reduces the number of rows to 11177.

I would appreciate any suggestion very much.

Homa