error import vcf to hierfstat #74

didier-aurelle · 2024-11-07T21:52:42Z

Hi,
I tried to import a vcf file to be analysed with hierfstat as follows:

read population definition file

popsEunicella <- read.csv("poplist_denovo_SNPfiltr.txt", sep = "", header = TRUE)

import vcf file

data <- read.vcf("RAD_spec_denovo_SNPfiltr.vcf")
data_genind <- loci2genind(data)
pop(data_genind) <- popsEunicella$POP
data_hierfstat <- genind2hierfstat(data_genind)

try to compute basic stats

bs_stats <- basic.stats(data_hierfstat, diploid = TRUE)

But when I try to compute some statistics, I get this error:

Erreur dans Class@package :
no applicable method for @ applied to an object of class "NULL"

Is there any mistake in my import?
Thanks
Didier

The text was updated successfully, but these errors were encountered:

jgx65 · 2024-11-08T08:27:48Z

Dear Didier, could you check the structure of your data object (str(data))? hierfstat::read.VCFor gaston::read.vcf creates gaston bed object . If you use pegas perhaps the problem is from this side?

Also the results of str(data_hierfstat) would be useful

Cheers

didier-aurelle · 2024-11-08T10:02:54Z

Hi Jérôme
thanks for your answer

So here are the results of the structure of the data (just the beginning in each case):

str(data)

Classes ‘loci’ and 'data.frame': 67 obs. of 10000 variables:
$ loc5_pos1 : Factor w/ 3 levels "C/C","./.","G/G": 1 1 1 1 2 1 1 1 1 1 ...
$ loc6_pos80 : Factor w/ 4 levels "A/A","G/A","G/G",..: 1 2 1 2 1 1 1 1 1 1 ...
$ loc7_pos69 : Factor w/ 5 levels "C/C","T/C","./.",..: 1 2 2 3 2 2 1 1 2 1 ...
$ loc8_pos8 : Factor w/ 3 levels "G/T","G/G","./.": 1 2 1 2 2 1 1 2 2 2 ...
$ loc10_pos5 : Factor w/ 5 levels "C/C","./.","T/C",..: 1 2 3 4 4 4 1 3 4 4 ...
$ loc12_pos0 : Factor w/ 3 levels "G/G","./.","G/A": 1 1 2 1 1 1 1 1 2 1 ...
$ loc14_pos122 : Factor w/ 5 levels "C/C","A/A","C/A",..: 1 2 2 2 2 2 2 3 1 2 ...
$ loc15_pos13 : Factor w/ 3 levels "T/T","./.","G/G": 1 2 1 2 1 2 1 1 1 1 ...
$ loc16_pos62 : Factor w/ 3 levels "T/T","./.","T/C": 1 2 1 2 1 1 1 1 1 1 ...
$ loc18_pos31 : Factor w/ 3 levels "G/G","./.","G/A": 1 2 1 1 1 1 1 1 1 1 ...
$ loc21_pos6 : Factor w/ 3 levels "T/T","T/C","C/C": 1 1 1 1 1 1 1 1 1 1 ...
$ loc23_pos62 : Factor w/ 5 levels "G/G","./.","G/A",..: 1 2 3 4 3 5 5 3 2 2 ...
$ loc25_pos14 : Factor w/ 5 levels "T/T","T/C","./.",..: 1 2 1 1 2 2 1 3 1 1 ...
$ loc27_pos27 : Factor w/ 3 levels "T/T","./.","T/C": 1 2 1 1 1 1 1 1 1 1 ...
$ loc28_pos21 : Factor w/ 5 levels "G/G","./.","G/T",..: 1 1 1 2 1 1 1 1 1 1 ...
$ loc34_pos9 : Factor w/ 4 levels "A/A","./.","G/A",..: 1 2 1 1 1 1 1 3 1 2 ...
$ loc35_pos96 : Factor w/ 5 levels "T/T","T/C","C/C",..: 1 1 2 1 1 2 1 1 2 1 ...
$ loc36_pos41 : Factor w/ 4 levels "T/T","./.","C/C",..: 1 2 1 1 3 2 1 1 1 1 ...
$ loc38_pos2 : Factor w/ 4 levels "G/G","./.","G/T",..: 1 2 1 1 1 1 1 1 1 1 ...
$ loc43_pos37 : Factor w/ 2 levels "G/G","G/A": 1 1 1 1 1 1 1 1 1 1 ...

str(data_hierfstat)

'data.frame': 67 obs. of 10001 variables:
$ pop : Factor w/ 4 levels "hybrid","cavolini",..: 1 1 1 1 1 1 1 1 1 2 ...
$ loc5_pos1 : int 22 22 22 22 NA 22 22 22 22 22 ...
$ loc6_pos80 : int 11 13 11 13 11 11 11 11 11 11 ...
$ loc7_pos69 : int 22 24 24 NA 24 24 22 22 24 22 ...
$ loc8_pos8 : int 34 33 34 33 33 34 34 33 33 33 ...
$ loc10_pos5 : int 22 NA 24 44 44 44 22 24 44 44 ...
$ loc12_pos0 : int 33 33 NA 33 33 33 33 33 NA 33 ...
$ loc14_pos122 : int 22 11 11 11 11 11 11 21 22 11 ...
$ loc15_pos13 : int 44 NA 44 NA 44 NA 44 44 44 44 ...
$ loc16_pos62 : int 44 NA 44 NA 44 44 44 44 44 44 ...
$ loc18_pos31 : int 33 NA 33 33 33 33 33 33 33 33 ...
$ loc21_pos6 : int 44 44 44 44 44 44 44 44 44 44 ...
$ loc23_pos62 : int 33 NA 31 NA 31 11 11 31 NA NA ...
$ loc25_pos14 : int 44 42 44 44 42 42 44 NA 44 44 ...
$ loc27_pos27 : int 44 NA 44 44 44 44 44 44 44 44 ...
$ loc28_pos21 : int 33 33 33 NA 33 33 33 33 33 33 ...
$ loc34_pos9 : int 11 NA 11 11 11 11 11 13 11 NA ...
$ loc35_pos96 : int 44 44 42 44 44 42 44 44 42 44 ...
$ loc36_pos41 : int 44 NA 44 44 22 NA 44 44 44 44 ...
$ loc38_pos2 : int 33 NA 33 33 33 33 33 33 33 33 ...
$ loc43_pos37 : int 33 33 33 33 33 33 33 33 33 33 ...
$ loc44_pos51 : int 42 44 44 44 44 44 44 44 44 44 ...

I tried with gaston as follows:

data2 <- read.VCF("RAD_spec_denovo_SNPfiltr.vcf", convert.chr = FALSE)

I got this file, but how can I use it with hierfstat now?

str(data2)

Formal class 'bed.matrix' [package "gaston"] with 8 slots
..@ ped :'data.frame': 67 obs. of 30 variables:
.. ..$ famid : chr [1:67] "EC-X-MFNB" "EC-X-MFNC" "EC-X-MFND" "EC-X-MFNE" ...
.. ..$ id : chr [1:67] "EC-X-MFNB" "EC-X-MFNC" "EC-X-MFND" "EC-X-MFNE" ...
.. ..$ father : num [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ mother : num [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ sex : num [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ pheno : logi [1:67] NA NA NA NA NA NA ...
.. ..$ N0 : int [1:67] 12622 7535 12816 11912 12045 12561 12749 12333 12432 11523 ...
.. ..$ N1 : int [1:67] 2223 1259 2075 2091 2091 1984 2097 2601 2655 1649 ...
.. ..$ N2 : int [1:67] 641 399 709 673 616 703 729 428 420 936 ...
.. ..$ NAs : int [1:67] 876 7169 762 1686 1610 1114 787 1000 855 2254 ...
.. ..$ N0.x : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ N1.x : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ N2.x : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ NAs.x : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ N0.y : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ N1.y : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ N2.y : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ NAs.y : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ N0.mt : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ N1.mt : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ N2.mt : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ NAs.mt : int [1:67] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ callrate : num [1:67] -Inf -Inf -Inf -Inf -Inf ...
.. ..$ hz : num [1:67] -2.538 -0.176 -2.723 -1.24 -1.299 ...
.. ..$ callrate.x : num [1:67] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ...
.. ..$ hz.x : num [1:67] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ...
.. ..$ callrate.y : num [1:67] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ...
.. ..$ hz.y : num [1:67] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ...
.. ..$ callrate.mt: num [1:67] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ...
.. ..$ hz.mt : num [1:67] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ...
..@ snps :'data.frame': 16362 obs. of 19 variables:
.. ..$ chr : chr [1:16362] "RAD_5" "RAD_6" "RAD_7" "RAD_8" ...
.. ..$ id : chr [1:16362] "loc5_pos1" "loc6_pos80" "loc7_pos69" "loc8_pos8" ...
.. ..$ dist : num [1:16362] 0 0 0 0 0 0 0 0 0 0 ...
.. ..$ pos : int [1:16362] 2 81 70 9 6 1 123 14 63 32 ...
.. ..$ A1 : chr [1:16362] "C" "A" "C" "G" ...
.. ..$ A2 : chr [1:16362] "G" "G" "T" "T" ...
.. ..$ quality : num [1:16362] 13 13 13 13 13 13 13 13 13 13 ...
.. ..$ filter : Factor w/ 1 level "PASS": 1 1 1 1 1 1 1 1 1 1 ...
.. ..$ N0 : int [1:16362] 54 51 23 55 24 56 52 48 58 58 ...
.. ..$ N1 : int [1:16362] 0 8 25 10 15 3 1 0 4 3 ...
.. ..$ N2 : int [1:16362] 4 3 15 0 23 0 4 7 0 0 ...
.. ..$ NAs : int [1:16362] 9 5 4 2 5 8 10 12 5 6 ...
.. ..$ N0.f : int [1:16362] NA NA NA NA NA NA NA NA NA NA ...
.. ..$ N1.f : int [1:16362] NA NA NA NA NA NA NA NA NA NA ...
.. ..$ N2.f : int [1:16362] NA NA NA NA NA NA NA NA NA NA ...
.. ..$ NAs.f : int [1:16362] NA NA NA NA NA NA NA NA NA NA ...
.. ..$ callrate: num [1:16362] 0.866 0.925 0.94 0.97 0.925 ...
.. ..$ maf : num [1:16362] 0.069 0.1129 0.4365 0.0769 0.4919 ...
.. ..$ hz : num [1:16362] 0 0.129 0.397 0.154 0.242 ...
..@ bed :
..@ p : num [1:16362] 0.069 0.1129 0.4365 0.0769 0.4919 ...
..@ mu : num [1:16362] 0.138 0.226 0.873 0.154 0.984 ...
..@ sigma : num [1:16362] 0.475 0.505 0.749 0.358 0.844 ...
..@ standardize_p : logi FALSE
..@ standardize_mu_sigma: logi FALSE

Didier

jgx65 · 2024-11-08T10:18:32Z

Thanks Didier.

So data_hierfstat has the correct structure for analyses with basic.stats. Where you able to obtain results from this function?

With data2, you can use fs.dosage(data2, pop=popsEunicella$POP) to obtain individuals and populations Fs

Best wishes

didier-aurelle · 2024-11-08T11:02:14Z

Thanks, it works with the fs.dosage function after import with gaston.
I would like to compute some population heterozygosities as well if possible.
With the data_hierfstat (after import with read.vcf from pegas then), basic.stats gives the error:

Erreur dans Class@package :
no applicable method for @ applied to an object of class "NULL"

Thanks!
Didier

jgx65 · 2024-11-08T11:39:27Z

Could you send a toy example dataset reproducing the error please? perhaps something like basic.stats(data_hierfstat[,1:30])? Alternatively, you can get nucleotide diversity from dosage data (pi.dosage), and if you pass for the argument L the number of SNPs, you will obtain heterozygosities

Cheers

didier-aurelle · 2024-11-08T11:46:40Z

yes, here is a subsampled dataset, which still gets the error
thanks
Didier

"" "pop" "loc5_pos1" "loc6_pos80" "loc7_pos69" "loc8_pos8" "loc10_pos5" "loc12_pos0" "loc14_pos122" "loc15_pos13" "loc16_pos62" "loc18_pos31" "loc21_pos6" "loc23_pos62" "loc25_pos14" "loc27_pos27" "loc28_pos21" "loc34_pos9" "loc35_pos96" "loc36_pos41" "loc38_pos2" "loc43_pos37" "loc44_pos51" "loc45_pos16" "loc46_pos7" "loc50_pos30" "loc53_pos31" "loc55_pos61" "loc57_pos12" "loc62_pos7" "loc65_pos1" "loc67_pos8"
"EC-X-MFNB" "hybrid" 22 11 22 34 22 33 22 44 44 33 44 33 44 44 33 11 44 44 33 33 42 33 22 22 11 33 22 22 44 22
"EC-X-MFNC" "hybrid" 22 13 24 33 NA 33 11 NA NA NA 44 NA 42 NA 33 NA 44 NA NA 33 44 NA 22 NA NA NA NA 22 44 22
"EC-X-MFND" "hybrid" 22 11 24 34 24 NA 11 44 44 33 44 31 44 44 33 11 42 44 33 33 44 33 22 23 NA 33 22 22 44 22
"EC-X-MFNE" "hybrid" 22 13 NA 33 44 33 11 NA NA 33 44 NA 44 44 NA 11 44 44 33 33 44 33 22 22 NA 33 22 NA 44 22
"EC-X-MFNF" "hybrid" NA 11 24 33 44 33 11 44 44 33 44 31 42 44 33 11 44 22 33 33 44 33 22 22 11 33 22 22 44 22
"EC-X-MFNG" "hybrid" 22 11 24 34 44 33 11 NA 44 33 44 11 42 44 33 11 42 NA 33 33 44 33 22 22 11 NA 22 22 44 22
"EC-X-MFNH" "hybrid" 22 11 22 34 22 33 11 44 44 33 44 11 44 44 33 11 44 44 33 33 44 33 22 23 11 33 22 22 44 22
"EC-X-MFNI" "hybrid" 22 11 22 33 24 33 21 44 44 33 44 31 NA 44 33 13 44 44 33 33 44 33 22 33 11 33 NA 22 44 22
"EC-X-MFNL" "hybrid" 22 11 24 33 44 NA 22 44 44 33 44 NA 44 44 33 11 42 44 33 33 44 33 22 23 11 33 22 22 44 21
"ECESC37" "cavolini" 22 11 22 33 44 33 11 44 44 33 44 NA 44 44 33 NA 44 44 33 33 44 33 22 22 NA 33 NA 22 44 22
"ECESC38" "cavolini" 22 11 22 33 44 33 11 44 44 33 44 11 44 44 33 NA 44 44 33 33 22 33 22 22 11 33 22 22 44 22
"ECESC39" "cavolini" 22 33 22 33 44 33 11 44 44 33 44 11 NA 44 33 11 44 44 33 33 44 33 NA 23 11 33 22 22 44 22
"ECMEL37" "cavolini" 22 NA 22 34 44 33 11 44 44 33 44 11 44 44 33 11 44 44 33 33 44 33 22 23 13 33 22 22 44 22
"ECPLD22" "cavolini" 22 11 22 33 44 33 11 44 44 33 44 11 44 44 33 11 44 44 33 33 44 33 22 22 11 33 22 22 44 22
"ECPLD23" "cavolini" NA 11 24 33 22 NA 11 44 44 33 44 31 44 44 33 11 44 44 33 33 44 33 22 22 11 33 22 22 44 22
"ECPLD24" "cavolini" 22 11 22 33 22 33 NA 44 44 33 44 11 44 44 33 13 44 44 33 33 44 33 22 23 11 33 22 22 44 22
"ECPLD25" "cavolini" 22 13 22 33 24 33 NA NA 44 33 44 11 44 44 33 33 44 44 33 33 44 NA 22 22 11 33 22 22 44 22
"ECPLD26" "cavolini" 22 13 24 33 24 NA 11 44 44 33 44 31 44 44 33 11 44 44 33 33 44 33 22 33 11 33 22 22 44 22
"ECPLD38" "cavolini" 22 11 44 33 44 33 11 44 44 33 44 11 44 44 33 11 44 44 33 33 44 33 22 33 11 33 22 22 44 22
"ECPLD39" "cavolini" 22 NA 22 33 24 33 11 44 NA 33 44 11 44 NA 33 13 44 44 33 31 44 33 22 23 11 33 22 NA 44 22
"ECRID13" "cavolini" NA 11 44 33 24 33 11 44 NA 33 44 11 44 44 33 11 44 22 33 33 44 33 22 23 11 33 22 22 44 22
"ECRID14" "cavolini" 22 13 NA 33 24 33 11 44 44 33 44 11 44 44 33 11 44 44 33 33 44 33 22 23 NA 33 22 22 44 22
"ECRID15" "cavolini" NA 11 24 33 44 33 11 44 44 33 44 31 44 44 33 11 44 44 33 33 44 33 22 22 11 33 22 22 44 22
"ECRID16" "cavolini" 22 33 24 33 44 33 11 44 44 33 44 11 44 NA 33 11 44 44 33 33 44 NA 22 33 13 33 22 22 NA 22
"ECRID17" "cavolini" 22 11 24 33 44 33 11 44 44 33 44 11 44 44 33 11 44 NA 33 33 44 33 22 23 13 33 22 22 44 22
"ECRID19" "cavolini" 22 13 24 33 24 33 11 44 44 NA 44 11 44 44 33 11 44 44 33 33 44 33 22 22 11 33 22 22 44 22
"ECRID20" "cavolini" NA 11 44 33 22 33 11 44 44 33 44 33 44 44 33 11 44 44 33 33 44 NA 22 NA 33 33 22 22 44 22
"ECRID21" "cavolini" 22 13 22 NA 22 NA 11 44 44 33 44 11 44 44 33 NA 44 42 33 33 42 33 22 33 11 33 22 22 44 22
"ECRID22" "cavolini" NA 11 24 33 NA 33 11 44 44 33 44 11 44 44 33 13 44 44 33 33 42 33 22 23 11 33 22 22 44 22
"ECRID23" "cavolini" 22 33 22 33 44 33 11 NA 44 33 44 11 44 44 33 11 44 44 33 33 42 33 22 33 NA 33 22 22 44 22
"ECRID25" "cavolini" 22 11 24 33 24 33 11 44 44 NA 44 11 44 44 33 11 44 44 33 33 42 33 22 33 13 33 22 22 44 22
"ECRID27" "cavolini" 22 11 44 33 24 33 11 44 44 33 44 11 44 44 33 11 44 NA 33 33 44 33 22 33 11 33 22 22 NA NA
"ECRID28" "cavolini" 22 11 24 33 24 33 11 44 44 33 44 11 44 44 33 11 44 NA 33 33 44 33 22 23 11 33 22 22 NA 22
"ECRID29" "cavolini" 22 11 24 33 44 33 11 44 44 33 44 31 44 44 33 11 44 42 33 33 44 33 22 33 11 33 22 22 44 22
"ES-X-MFNA" "hybrid" 22 11 24 34 24 33 11 NA 44 33 44 33 NA 44 33 11 44 44 33 33 44 33 22 23 13 33 22 22 44 22
"ES-X-MFNJ" "hybrid" 22 11 22 33 24 NA NA 44 44 33 44 31 44 44 33 13 42 44 33 31 42 NA 22 NA 11 33 22 22 44 21
"ES-X-MFNK" "hybrid" 22 11 44 34 22 NA NA 44 44 33 44 33 44 44 34 11 44 44 33 33 44 33 22 22 11 33 22 22 44 22
"ESFRO10" "singularis" 22 13 22 33 24 33 NA NA 44 33 44 33 42 44 33 11 42 42 33 33 44 33 22 33 11 NA 22 22 44 22
"ESFRO11" "singularis" 22 11 22 33 22 33 NA 44 44 33 44 33 44 44 33 11 42 42 33 33 44 33 22 22 11 33 NA 22 44 22
"ESFRO12" "singularis" NA 11 24 33 22 33 NA 44 44 33 44 33 44 44 33 11 42 44 33 33 44 33 22 22 11 33 22 22 44 22
"ESFRO13" "singularis" 22 11 44 33 22 33 11 NA 44 33 44 33 42 44 33 11 44 44 33 33 44 33 22 22 11 33 22 NA 44 22
"ESFRO14" "singularis" NA NA 24 33 22 33 11 44 44 33 44 31 42 44 34 11 22 22 33 33 44 31 22 22 11 33 22 22 44 22
"ESFRO15" "singularis" NA 11 24 33 22 33 11 44 44 33 44 33 NA 44 33 11 42 44 33 33 44 33 22 22 11 33 22 22 44 22
"ESFRO2" "singularis" 22 11 22 33 22 33 22 44 44 33 44 33 42 44 34 11 42 44 33 33 44 33 22 22 11 33 22 NA 44 22
"ESFRO3" "singularis" 22 11 22 33 22 33 11 NA NA 33 44 33 44 NA 33 11 42 44 33 33 44 33 22 22 NA 33 NA 22 44 22
"ESFRO5" "singularis" 22 11 44 33 22 33 22 44 44 33 44 33 NA 44 33 13 44 42 33 33 44 NA 22 23 11 33 NA 22 44 22
"ESFRO6" "singularis" 22 11 NA 33 24 33 11 NA 44 33 44 31 44 44 33 11 42 44 33 33 44 33 22 22 11 33 22 22 44 22
"ESFRO7" "singularis" 22 11 22 34 22 33 11 44 44 33 44 33 NA 44 33 11 NA 42 33 33 44 33 NA 22 11 33 22 22 44 22
"ESFRO8" "singularis" 22 11 22 33 22 31 11 NA 44 33 44 33 44 44 33 11 44 42 33 33 44 33 22 22 NA 33 22 22 44 21
"ESFRO9" "singularis" 22 11 24 NA 22 33 11 44 44 33 44 31 NA 44 33 11 44 42 33 33 44 33 22 22 11 33 22 22 44 22
"ESSFI1" "singularis" 22 11 24 33 NA 33 NA 44 44 33 44 33 44 44 33 11 22 44 33 31 44 33 22 22 11 NA 22 22 44 22
"ESSFI10" "singularis" 22 11 24 33 22 33 11 44 44 33 44 33 44 44 33 11 44 42 33 33 44 33 22 NA 11 33 22 NA 44 22
"ESSFI2" "singularis" 22 11 22 33 22 33 11 44 44 33 44 33 NA 44 33 11 44 44 33 33 44 33 22 NA 11 33 NA 22 44 22
"ESSFI3" "singularis" 22 11 44 33 22 33 11 44 44 31 44 33 44 44 33 11 44 42 33 33 44 NA 22 22 11 33 22 22 NA 22
"ESSFI4" "singularis" 22 11 44 33 NA NA 11 44 44 NA 44 33 NA 44 33 11 44 22 33 33 44 NA 22 NA 11 33 22 22 44 22
"ESSFI5" "singularis" 22 11 44 34 22 33 11 44 44 33 44 33 44 44 33 11 44 22 33 33 44 33 NA 22 11 33 22 22 44 NA
"ESSFI6" "singularis" 22 11 22 33 22 31 11 44 44 31 44 33 22 44 33 11 44 42 33 33 44 31 22 NA 11 NA 22 NA 44 22
"ESSFI7" "singularis" 22 11 24 34 44 31 11 44 44 31 44 33 42 44 33 11 42 42 33 33 44 NA 22 22 11 33 22 22 44 NA
"ESSFI8" "singularis" 22 NA 24 33 NA 33 NA NA 44 NA 44 33 42 44 NA 11 NA 44 33 33 44 31 22 NA NA 33 NA NA 44 22
"ESSFI9" "singularis" 22 11 24 33 22 33 NA 44 44 33 44 31 44 44 33 NA 44 44 33 31 44 33 22 22 NA 33 22 22 NA 22
"EVCSO2" "verrucosa" 33 NA 44 33 44 33 11 33 42 33 42 33 42 44 44 11 44 44 34 33 44 33 NA 33 11 11 NA NA 41 22
"EVCSO4" "verrucosa" 22 11 22 33 44 33 11 33 42 33 42 NA 44 42 44 NA 44 44 33 33 44 33 NA 33 11 11 24 33 41 22
"EVFRO1" "verrucosa" 33 11 44 33 44 33 11 33 42 33 44 33 44 44 44 11 44 44 33 33 44 33 21 33 11 11 44 33 44 22
"EVFRO2" "verrucosa" 33 11 44 33 44 33 11 33 44 NA 22 33 44 44 NA 11 44 44 33 33 44 33 21 NA 11 11 44 33 44 22
"EVFRO3" "verrucosa" 22 11 NA 33 44 33 11 33 42 33 22 33 44 44 44 11 44 44 33 33 44 33 22 33 11 11 NA 33 41 22
"EVFRO4" "verrucosa" 33 11 44 33 44 33 11 33 44 33 42 33 44 44 44 11 44 NA NA 33 44 33 21 33 11 11 44 33 41 22
"EVFRO5" "verrucosa" 22 11 44 33 44 33 11 33 44 33 44 NA 44 42 44 11 44 44 33 33 44 NA 21 33 11 11 44 NA NA 22

jgx65 · 2024-11-08T12:00:37Z

aurelle_toy.txt
It works for me:

> dat<-read.table("aurelle_toy.txt",header=TRUE)
> str(dat)
'data.frame':	67 obs. of  31 variables:
 $ pop         : chr  "hybrid" "hybrid" "hybrid" "hybrid" ...
 $ loc5_pos1   : int  22 22 22 22 NA 22 22 22 22 22 ...
 $ loc6_pos80  : int  11 13 11 13 11 11 11 11 11 11 ...
 $ loc7_pos69  : int  22 24 24 NA 24 24 22 22 24 22 ...
 $ loc8_pos8   : int  34 33 34 33 33 34 34 33 33 33 ...
 $ loc10_pos5  : int  22 NA 24 44 44 44 22 24 44 44 ...
 $ loc12_pos0  : int  33 33 NA 33 33 33 33 33 NA 33 ...
 $ loc14_pos122: int  22 11 11 11 11 11 11 21 22 11 ...
 $ loc15_pos13 : int  44 NA 44 NA 44 NA 44 44 44 44 ...
 $ loc16_pos62 : int  44 NA 44 NA 44 44 44 44 44 44 ...
 $ loc18_pos31 : int  33 NA 33 33 33 33 33 33 33 33 ...
 $ loc21_pos6  : int  44 44 44 44 44 44 44 44 44 44 ...
 $ loc23_pos62 : int  33 NA 31 NA 31 11 11 31 NA NA ...
 $ loc25_pos14 : int  44 42 44 44 42 42 44 NA 44 44 ...
 $ loc27_pos27 : int  44 NA 44 44 44 44 44 44 44 44 ...
 $ loc28_pos21 : int  33 33 33 NA 33 33 33 33 33 33 ...
 $ loc34_pos9  : int  11 NA 11 11 11 11 11 13 11 NA ...
 $ loc35_pos96 : int  44 44 42 44 44 42 44 44 42 44 ...
 $ loc36_pos41 : int  44 NA 44 44 22 NA 44 44 44 44 ...
 $ loc38_pos2  : int  33 NA 33 33 33 33 33 33 33 33 ...
 $ loc43_pos37 : int  33 33 33 33 33 33 33 33 33 33 ...
 $ loc44_pos51 : int  42 44 44 44 44 44 44 44 44 44 ...
 $ loc45_pos16 : int  33 NA 33 33 33 33 33 33 33 33 ...
 $ loc46_pos7  : int  22 22 22 22 22 22 22 22 22 22 ...
 $ loc50_pos30 : int  22 NA 23 22 22 22 23 33 23 22 ...
 $ loc53_pos31 : int  11 NA NA NA 11 11 11 11 11 NA ...
 $ loc55_pos61 : int  33 NA 33 33 33 NA 33 33 33 33 ...
 $ loc57_pos12 : int  22 NA 22 22 22 22 22 NA 22 NA ...
 $ loc62_pos7  : int  22 22 22 NA 22 22 22 22 22 22 ...
 $ loc65_pos1  : int  44 44 44 44 44 44 44 44 44 44 ...
 $ loc67_pos8  : int  22 22 22 22 22 22 22 22 21 22 ...
> bs<-basic.stats(dat)
> bs
$perloc
                 Ho     Hs     Ht     Dst    Htp    Dstp     Fst
loc5_pos1    0.0000 0.1336 0.2477  0.1141 0.2857  0.1521  0.4606
loc6_pos80   0.1079 0.1489 0.1602  0.0113 0.1639  0.0151  0.0705
loc7_pos69   0.3428 0.4489 0.5060  0.0571 0.5250  0.0761  0.1128
loc8_pos8    0.1695 0.1400 0.1562  0.0162 0.1616  0.0216  0.1035
loc10_pos5   0.2097 0.2991 0.4933  0.1942 0.5581  0.2589  0.3936
loc12_pos0   0.0341 0.0332 0.0339  0.0007 0.0341  0.0009  0.0194
loc14_pos122 0.0250 0.1582 0.1701  0.0118 0.1740  0.0158  0.0696
loc15_pos13  0.0000 0.0000 0.3750  0.3750 0.5000  0.5000  1.0000
loc16_pos62  0.1429 0.1048 0.1333  0.0285 0.1429  0.0380  0.2140
loc18_pos31  0.0357 0.0346 0.0354  0.0008 0.0357  0.0011  0.0231
loc21_pos6   0.1071 0.1310 0.2202  0.0893 0.2500  0.1190  0.4052
loc23_pos62  0.1963 0.2310 0.4592  0.2282 0.5353  0.3043  0.4970
loc25_pos14  0.1989 0.1951 0.2043  0.0093 0.2074  0.0123  0.0453
loc27_pos27  0.0714 0.0635 0.0694  0.0060 0.0714  0.0080  0.0860
loc28_pos21  0.0455 0.0453 0.3972  0.3519 0.5145  0.4691  0.8859
loc34_pos9   0.0909 0.1083 0.1085  0.0003 0.1086  0.0004  0.0026
loc35_pos96  0.1786 0.1785 0.2024  0.0239 0.2103  0.0318  0.1180
loc36_pos41  0.1314 0.2128 0.2364  0.0235 0.2442  0.0314  0.0996
loc38_pos2   0.0417 0.0398 0.0412  0.0014 0.0417  0.0019  0.0337
loc43_pos37  0.0526 0.0526 0.0517 -0.0009 0.0514 -0.0012 -0.0173
loc44_pos51  0.0817 0.0952 0.0976  0.0023 0.0983  0.0031  0.0241
loc45_pos16  0.0395 0.0380 0.0391  0.0011 0.0395  0.0014  0.0278
loc46_pos7   0.2000 0.1221 0.1805  0.0585 0.2000  0.0779  0.3238
loc50_pos30  0.2076 0.2844 0.5030  0.2186 0.5758  0.2914  0.4345
loc53_pos31  0.0732 0.0898 0.0925  0.0027 0.0934  0.0036  0.0295
loc55_pos61  0.0000 0.0000 0.3750  0.3750 0.5000  0.5000  1.0000
loc57_pos12  0.0500 0.0472 0.3493  0.3021 0.4500  0.4028  0.8649
loc62_pos7   0.0000 0.0000 0.3750  0.3750 0.5000  0.5000  1.0000
loc65_pos1   0.1667 0.1137 0.1534  0.0397 0.1667  0.0529  0.2588
loc67_pos8   0.0536 0.0518 0.0526  0.0008 0.0529  0.0011  0.0160
                Fstp     Fis    Dest
loc5_pos1     0.5324  1.0000  0.1756
loc6_pos80    0.0918  0.2751  0.0177
loc7_pos69    0.1449  0.2364  0.1380
loc8_pos8     0.1335 -0.2104  0.0251
loc10_pos5    0.4640  0.2991  0.3695
loc12_pos0    0.0256 -0.0263  0.0009
loc14_pos122  0.0907  0.8420  0.0188
loc15_pos13   1.0000     NaN  0.5000
loc16_pos62   0.2663 -0.3630  0.0425
loc18_pos31   0.0305 -0.0315  0.0011
loc21_pos6    0.4760  0.1821  0.1369
loc23_pos62   0.5685  0.1504  0.3957
loc25_pos14   0.0595 -0.0198  0.0153
loc27_pos27   0.1115 -0.1255  0.0085
loc28_pos21   0.9119 -0.0028  0.4914
loc34_pos9    0.0035  0.1603  0.0004
loc35_pos96   0.1514 -0.0005  0.0388
loc36_pos41   0.1285  0.3825  0.0399
loc38_pos2    0.0445 -0.0466  0.0019
loc43_pos37  -0.0233  0.0004 -0.0013
loc44_pos51   0.0318  0.1422  0.0035
loc45_pos16   0.0367 -0.0381  0.0015
loc46_pos7    0.3897 -0.6386  0.0888
loc50_pos30   0.5061  0.2699  0.4072
loc53_pos31   0.0389  0.1845  0.0040
loc55_pos61   1.0000     NaN  0.5000
loc57_pos12   0.8951 -0.0592  0.4228
loc62_pos7    1.0000     NaN  0.5000
loc65_pos1    0.3177 -0.4656  0.0597
loc67_pos8    0.0212 -0.0344  0.0012

$overall
    Ho     Hs     Ht    Dst    Htp   Dstp    Fst   Fstp    Fis 
0.1018 0.1201 0.2173 0.0973 0.2498 0.1297 0.4476 0.5193 0.1520 
  Dest 
0.1474

didier-aurelle · 2024-11-08T12:45:04Z

Very strange: I reinstalled the packages, downloaded your file (my toy file!), imported with read.table and it works!
but with the original file, I still get the error... I will try to workaround with the ped format
thanks
Didier

jgx65 · 2024-11-08T13:56:07Z

Perhaps try saving your file as text and reimport it?
Best

didier-aurelle · 2024-11-08T15:49:00Z

Yes, I tried but it didn't work. Maybe this is link to the OS? I work on Linux
thanks

jgx65 · 2024-11-08T16:35:38Z

I don't think the OS matters. Perhaps the first column, containing names (e.g. "EC-X-MFNB") is misinterpreted. try removing it, or removing the "" with write.table(data_hierfstat,file="test.txt",quote=FALSE,row.names=FALSE,sep="\t")

jgx65 · 2024-11-12T09:49:54Z

Hi @didier-aurelle , did you manage to solve the issue? If so, can I close it? Thanks!

didier-aurelle · 2024-11-12T10:21:42Z

Hi
I have just tried to export in text and then reimport as you proposed, without sample names then, and it doesn't work. Still the same error
Erreur dans Class@package :
no applicable method for @ applied to an object of class "NULL"
Didier

didier-aurelle · 2024-11-12T10:35:32Z

an update: some functions work. For example allele.count, allelic.richness,
Does not work for example: genet.dist, pop.freq
Didier

jgx65 · 2024-11-12T12:14:29Z

Could you send me a toy example (file+commands) in order for me to replicate the error?
Thanks!

didier-aurelle · 2024-11-12T12:32:07Z

toy_30SNPs.vcf.txt
poplist_denovo_SNPfiltr.txt

Yes, I attach the vcf file (renamed .txt to allow attachment) and the pop definition file, the script is below
thanks
Didier

library(adegenet)
library(hierfstat)
library(pegas)

setwd("~/Nextcloud2/Speciation_Eunicella/RAD_speciation_reference/denovo/")

popsEunicella <- read.table("poplist_denovo_SNPfiltr.txt", header = TRUE)
popsEunicella2 <- as.factor(popsEunicella$POP)
View(popsEunicella)

read vcf file

data <- read.vcf("toy_30SNPs.vcf")
data_genind <- loci2genind(data)
data_genind$pop <- popsEunicella2
pop(data_genind)
data_hierfstat <- genind2hierfstat(data_genind)

bs_stats <- basic.stats(data_hierfstat, diploid = TRUE)

jgx65 · 2024-11-12T17:18:43Z

OK, I think I found the problem, it was in function hierfstat::pop.freq . I've pushed a new version to github. Try reinstalling hierfstat from github, and re-running, things should work.

Many thanks for pointing the issue, if you're happy with the results, you can close it

didier-aurelle · 2024-11-13T15:20:49Z

Yes, it works now!
merci!
Didier

didier-aurelle closed this as completed Nov 13, 2024

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error import vcf to hierfstat #74

error import vcf to hierfstat #74

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error import vcf to hierfstat #74

error import vcf to hierfstat #74

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didier-aurelle commented Nov 7, 2024

read population definition file

import vcf file

try to compute basic stats

jgx65 commented Nov 8, 2024

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read vcf file

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