Place microsatellites in the correct order for genind objects.

resort_microsatellites.R

resort_microsat <- function(x){
	# Gather all alleles, convert to numeric, and reorder
	alls <- adegenet::alleles(x)
	alln <- lapply(alls, as.numeric)
	alln <- lapply(alln, order)
	
	# Loop over the names and paste together the locus name and the sorted alleles.
	alls <- lapply(names(alls), function(i) paste(i, alls[[i]][ alln[[i]] ], sep = "."))
	
	# Convert to a vector an match the name to the column names of the data matrix. 
	cols <- unlist(alls, use.names = FALSE)
	cols <- match(cols, colnames(tab(x)))
	return(x[, cols])
}

Here's a small working demonstration

library("adegenet")
library("pegas")
myFile <- system.file("files/nancycats.gtx",package="adegenet")
cats <- import2genind(myFile)

## 
##  Converting data from GENETIX to a genind object... 
## 
## ...done.

This works:

data(nancycats)
hw.test(nancycats, B=0)

##           chi^2  df  Pr(chi^2 >)
## fca8  395.80006 120 0.000000e+00
## fca23 239.34221  55 0.000000e+00
## fca43 434.33397  45 0.000000e+00
## fca45  66.11849  36 1.622163e-03
## fca77 270.52066  66 0.000000e+00
## fca78 402.80002  28 0.000000e+00
## fca90 217.19836  66 0.000000e+00
## fca96 193.36764  66 1.965095e-14
## fca37 291.00731 153 1.209777e-10

This has problems:

hw.test(cats, B=0)

## Warning in O - E: longer object length is not a multiple of shorter object
## length

## Warning in (O - E)^2/E: longer object length is not a multiple of shorter
## object length

## Warning in O - E: longer object length is not a multiple of shorter object
## length

## Warning in (O - E)^2/E: longer object length is not a multiple of shorter
## object length

## Warning in O - E: longer object length is not a multiple of shorter object
## length

## Warning in (O - E)^2/E: longer object length is not a multiple of shorter
## object length

## Warning in O - E: longer object length is not a multiple of shorter object
## length

## Warning in (O - E)^2/E: longer object length is not a multiple of shorter
## object length

## Warning in O - E: longer object length is not a multiple of shorter object
## length

## Warning in (O - E)^2/E: longer object length is not a multiple of shorter
## object length

## Warning in O - E: longer object length is not a multiple of shorter object
## length

## Warning in (O - E)^2/E: longer object length is not a multiple of shorter
## object length

## Warning in O - E: longer object length is not a multiple of shorter object
## length

## Warning in (O - E)^2/E: longer object length is not a multiple of shorter
## object length

## Warning in O - E: longer object length is not a multiple of shorter object
## length

## Warning in (O - E)^2/E: longer object length is not a multiple of shorter
## object length

## Warning in O - E: longer object length is not a multiple of shorter object
## length

## Warning in (O - E)^2/E: longer object length is not a multiple of shorter
## object length

##             chi^2  df  Pr(chi^2 >)
## fca8  46504.45655 120 0.000000e+00
## fca23  2023.71668  55 0.000000e+00
## fca43  7957.23992  45 0.000000e+00
## fca45    93.25975  36 5.681616e-07
## fca77 21636.11122  66 0.000000e+00
## fca78  1072.03868  28 0.000000e+00
## fca90 11361.25571  66 0.000000e+00
## fca96   825.46134  66 0.000000e+00
## fca37  2283.46490 153 0.000000e+00

This fixes everything:

hw.test(resort_microsat(cats), B=0)

##           chi^2  df  Pr(chi^2 >)
## fca8  395.80006 120 0.000000e+00
## fca23 239.34221  55 0.000000e+00
## fca43 434.33397  45 0.000000e+00
## fca45  66.11849  36 1.622163e-03
## fca77 270.52066  66 0.000000e+00
## fca78 402.80002  28 0.000000e+00
## fca90 217.19836  66 0.000000e+00
## fca96 193.36764  66 1.965095e-14
## fca37 291.00731 153 1.209777e-10