I am unable to convert a *.str file into a genind object using the read.structure() command. If I use original "nancycats.str", it works, whereas for any other file it does not. If I try to fool by pasting my file into nancycats.str, it goes till conversion but doesn't convert. But when I revert to original "nancycats.str", it works well.
Modifications tried:
Shortcut for path:
obj1 <- read.structure(system.file("files/Adadig_ImpNgb.str",package="adegenet"))
Error in if (!toupper(.readExt(file)) %in% c("STR", "STRU")) stop("File extension .stru expected") :
argument is of length zero
In addition: Warning messages:
1: package ‘adegenet’ was built under R version 4.4.2
2: package ‘ade4’ was built under R version 4.4.2
Providing a full path:
obj1 <- read.structure("C:/Users/PHendre/OneDrive - CIFOR-ICRAF/Documents/R/win-library/4.0/adegenet/files/Adadig_ImpNgb.str", package="adegenet")
Error in read.structure("C:/Users/PHendre/OneDrive - CIFOR-ICRAF/Documents/R/win-library/4.0/adegenet/files/Adadig_ImpNgb.str", :
unused argument (package = "adegenet")
Same "nancycats.str" relabelled as "nancycatsdupl.str" without changing anything
obj1 <- read.structure(system.file("files/nancycatsdupl.str",package="adegenet"))
Error in if (!toupper(.readExt(file)) %in% c("STR", "STRU")) stop("File extension .stru expected") :
argument is of length zero
Pasting the infile into "nancycats.str" following error:
obj1 <- read.structure(system.file("files/nancycats.str",package="adegenet"))
How many genotypes are there?
320
How many markers are there?
509
Which column contains labels for genotypes ('0' if absent)?
1
Which column contains the population factor ('0' if absent)?
0
Which other optional columns should be read (press 'return' when done)?
1:
Which row contains the marker names ('0' if absent)?
0
Are genotypes coded by a single row (y/n)?
n
Converting data from a STRUCTURE .stru file to a genind object...
Error in txt[(lastline - n + 1):lastline] :
only 0's may be mixed with negative subscripts
The original "nancycats.str" (removing populaiton factor line)
obj1 <- read.structure(system.file("files/nancycats.str",package="adegenet"))
How many genotypes are there?
237
How many markers are there?
9
Which column contains labels for genotypes ('0' if absent)?
1
Which column contains the population factor ('0' if absent)?
0
Which other optional columns should be read (press 'return' when done)?
1:
Which row contains the marker names ('0' if absent)?
0
Are genotypes coded by a single row (y/n)?
n
Converting data from a STRUCTURE .stru file to a genind object...