I'm using the read.structure function in the adegenet package to analyze some genetics data, and need to include spatial coordinates in the genid object so I can run a landscape genetics analysis. Adegent package states that a column/s to be included in the other slot should be referenced using "a vector of integers giving the indexes of the columns containing other informations to be read. Will be available in @other of the created object. " However, so far I have been unsuccessful in my coding to produce the correct genid object.
Can anyone assist me with this?
Add the spatial coordinates separate from the genotype data. Create the genind with the genotype data first, then import the spatial coordinates into a separate data frame. Then direct those coordinates into the "other" slot. Here is an example (assumes a tab-delimited text file):
Coord
Hi Joshua
My preferred solution is to use the function read.genedata from library PopGenReport. (but be cautious with variable and individual names, too often they cause problems unless you follow the instructions in the vignette),
Cheers
Pablo
put the lat and long coordinates in separate columns. Eg. col1=genotype ID, col2=population ID, col3=lat, col4=long. Specify 3 and 4 when prompted with "Which other optional columns should be read (press 'return' when done)? "
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