Description Usage Arguments Value Examples
This function converts a raw vcf file to a genind object with the assumptions that (1) the ploidy is 2 (but will work with one actually, but not with ploidy > 2) and (2) marker is codominant (duhhhhhh, it should be!!!) this basically creates an allele frequency table from the vcf which is the used as the tab in a genind object. Then, the output is wrapped using the genind function from adegenet together with other auxillary information.
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filePath |
full path to the vcf file; this calls the vcfLoad |
pop |
vector of the the popID of each sample |
dataIn |
data.table obtained using vcfLoad function |
... |
other parameters needed by genind type object, see genind or df2genind |
A genind class object to be used by adegenet
1 2 3 4 | # reads the example.vcf and makes a genind object
vcfGenind <- vcf2genind("example.vcf")
populationData <- read.table("populationMetadata")
findfixedSNP(dataIn = vcfInput, popinfo = populationData)
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