I'm trying to run the function genetic_diff(): myDiff <- genetic_diff(vcf, pops = pop, method = 'nei')
But I get the following information " if(class(x) != "vcfR"){ stop(paste("Expecting an object of class vcfR, instead received", class(vcf)))"
What can I do?
Presumably you have a vcfR file. Use the read.vcfR command to read it as a vcfR file, then you can successfully run the genetic_diff command. An example using the vcfR example file lumpy.vcf.
x=read.vcfR("filename.txt")
pop=as.factor(c("a", "a", "b"))
genetic_diff(x, pop, method="nei")
CHROM POS Hs_a Hs_b Ht n_a n_b Gst Htmax Gstmax Gprimest
1 chr1 93822813 0.5 0.0 0.4444444 4 2 0.25 0.6666667 0.5000000 0.5
2 chr12 71315481 0.5 NaN 0.5000000 4 0 NaN 0.5000000 NaN NaN
3 chr12 71315764 0.5 NaN 0.5000000 4 0 NaN 0.5000000 NaN NaN
4 chr12 71316537 0.5 NaN 0.5000000 4 0 NaN 0.5000000 NaN NaN
5 chr12 71316539 0.5 NaN 0.5000000 4 0 NaN 0.5000000 NaN NaN
6 chr13 33618456 0.5 0.5 0.5000000 2 2 0.00 0.7500000 0.3333333 0.0
7 chr15 70302685 0.5 NaN 0.5000000 4 0 NaN 0.5000000 NaN NaN
8 chr16 25192730 0.5 0.5 0.5000000 4 2 0.00 0.7222222 0.3076923 0.0
9 chr16 25192895 0.5 0.5 0.5000000 4 2 0.00 0.7222222 0.3076923 0.0
10 chr16 25193026 0.5 0.5 0.5000000 4 2 0.00 0.7222222 0.3076923 0.0
11 chr16 25193261 0.5 0.5 0.5000000 4 2 0.00 0.7222222 0.3076923 0.0