read.genalex will read in a genalex-formatted file that has been exported in
a comma separated format and will parse most types of genalex data. The
output is a
a *.csv file exported from genalex
indicate the ploidy of the dataset
indicates the presence of geographic data in the file. This data
will be included in a data frame labeled
indicates the presence of regional data in the file.
A character specifying the column separator of the data. Defaults to ",".
For polyploid data: Do you want to recode your data to
have varying ploidy? Default is
genclone = FALSE
The resulting genind object
will have a data frame in the
other slot called
population_hierarchy. This will contain a column for your population
data and a column for your Regional data if you have set the flag.
genclone = TRUE
The resulting genclone object will
have a single strata defined in the strata slot. This will
be called "Pop" and will reflect the population factor defined in the
genalex input. If
region = TRUE, a second column will be inserted
and labeled "Region". If you have more than two strata within
your data set, you should run the command
your data set to define the unique stratifications.
The genind object has an all-or-none approach to missing data. If a sample has missing data at a particular locus, then the entire locus is considered missing. This works for diploids and haploids where allelic dosage is unambiguous. For polyploids this poses a problem as much of the data set would be transformed into missing data. With this function, I have created a workaround.
When importing polyploid data sets, missing data is scored as "0" and kept within the genind object as an extra allele. This will break most analyses relying on allele frequencies*. All of the functions in poppr will work properly with these data sets as multilocus genotype analysis is agnostic of ploidy and we have written both Bruvo's distance and the index of association in such a way as to be able to handle polyploids presented in this manner.
* To restore functionality of analyses relying on allele frequencies, use
This function cannot handle raw allele frequency data.
In the case that there are duplicated names within the file, this function
will assume separate individuals and rename each one to a sequence of
integers from 1 to the number of individuals. A vector of the original
names will be saved in the
other slot under
Zhian N. Kamvar
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## Not run: Aeut <- read.genalex(system.file("files/rootrot.csv", package="poppr")) genalex2 <- read.genalex("genalex2.csv", geo=TRUE) # A genalex file with geographic coordinate data. genalex3 <- read.genalex("genalex3.csv", region=TRUE) # A genalex file with regional information. genalex4 <- read.genalex("genalex4.csv", region=TRUE, geo=TRUE) # A genalex file with both regional and geographic information. ## End(Not run)
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