Description Usage Arguments Details Value Note Author(s) See Also Examples
View source: R/file_handling.r
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 genclone-class or genind-class object.
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a \*.csv file exported from genalex
an integer to 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
The resulting genclone-class or genind-class
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
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
adegenet::splitStrata() on your data set to define the
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
A genclone or genind bject.
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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