You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Dear Dr Zheng,
I am trying to add a node to my GDA file, but I am struggling a lot with it, so I would love some advice and help with this.
I obtained my GDS file by converting a "genlight" object (R package adegenet/dartR) into a GDS file for SNPRelate with the dartR::gl2gds() function.
However, the GDS file has no sample annotation, and I would like to add this as I would like to run KING robust incluging the family.id field (geographic population or hybrids/pure individuals categories).
I have read your SNPRelate tutorial, but I am encountering troubles adding a gds node to my GDS object.
Here is the code I used:
Dear Dr Zheng,
I am trying to add a node to my GDA file, but I am struggling a lot with it, so I would love some advice and help with this.
I obtained my GDS file by converting a "genlight" object (R package adegenet/dartR) into a GDS file for SNPRelate with the dartR::gl2gds() function.
However, the GDS file has no sample annotation, and I would like to add this as I would like to run KING robust incluging the family.id field (geographic population or hybrids/pure individuals categories).
I have read your SNPRelate tutorial, but I am encountering troubles adding a gds node to my GDS object.
Here is the code I used:
"
mydataset_GDS = gl2gds(
mydataset_genlight,
outfile = "mydataset_GDS.gds",
outpath = getwd(),
snp_pos = "0",
snp_chr = "0",
chr_format = "character",
verbose = 5)
sample.annotation = mydataset_genlight@other$ind.metrics # contains all individual metrics in a dataframe format
class(sample.annotation) # data.frame
I don't know how else to include the sample/individuals metadata in the GDS file. I would really appreciate some help!
Thanks a lot!
Best,
Gabriella
The text was updated successfully, but these errors were encountered: