Hello, I have probably very simple problem, but I can't find the solution... :-( I wish to make bootstraped tree of attached microsatellite diploid data. It works fine with DNA sequences and I was using same code last year and it was working. :-)
library(pegas)
library(ape)
LOCI <- read.loci("ssrs.txt", header=TRUE, loci.sep="\t", allele.sep="/",
col.pop=2, col.loci=3:14, row.names=1)
# Looks OK
GENIND <- loci2genind(LOCI)
DIST <- dist(x=GENIND, method="euclidean", diag=TRUE, upper=TRUE)
NJ <- nj(DIST)
BOOT <- boot.phylo(phy=NJ, x=LOCI, FUN=function(X) nj(dist(loci2genind(X))),
B00)
|| 1%Error in df2genind(as.matrix(x[, attr(x, "locicol")]), sep = "[/\\|]",
:
length of factor pop differs from nrow(X)
Any idea what could went wrong?
Thank You,
Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/
Institute of Botany, Academy of Science
Zámek 1, Průhonice, 25243, CZ
http://www.ibot.cas.cz/en/
Czech Republic
pop L01 L02 L03 L04 L05 L06 L07 L08 L09 L10 L11 L12 I01 A 269/269 198/198 221/223 419/419 197/197 196/196 237/251 163/163 211/233 132/136 279/291 150/152 I02 A 275/283 198/198 221/223 419/419 193/193 168/190 243/251 163/163 211/215 128/136 293/293 150/152 I03 A 275/299 198/198 221/223 419/419 193/197 190/196 237/243 163/163 215/233 132/136 279/293 150/152 I04 A 275/275 198/198 221/221 419/419 193/193 168/196 243/251 163/163 215/215 128/136 279/293 150/152 I05 A 275/275 198/198 221/221 419/419 193/193 168/196 243/251 163/163 215/215 128/136 279/293 150/152 I06 A 275/293 198/198 221/223 419/421 193/193 190/196 243/243 163/195 215/215 128/130 283/291 150/152 I07 A 275/299 198/198 211/211 419/419 197/197 168/196 243/251 163/163 211/215 128/136 279/291 150/150 I08 A 275/275 198/180 211/211 419/419 193/193 168/190 237/243 163/163 215/215 130/136 277/291 150/150 I09 A 283/283 198/180 211/221 399/419 193/193 190/196 237/243 163/163 219/227 132/136 279/291 152/152 I10 A 275/275 198/180 221/223 419/419 193/193 168/190 237/243 163/163 215/215 130/136 277/293 150/150 I11 A 275/299 198/198 211/221 419/419 193/197 190/196 237/243 163/163 215/233 132/136 279/293 150/152 I12 A 275/299 198/198 221/223 419/419 193/197 190/196 237/243 163/163 215/233 132/136 279/293 150/152 I13 A 275/283 198/198 221/223 419/419 193/193 168/190 243/251 163/163 209/215 128/136 293/293 150/152 I14 B 227/227 198/198 221/231 397/415 193/195 182/182 237/237 195/187 201/201 122/128 293/293 152/192 I15 B 299/327 198/180 221/223 399/419 193/195 168/190 237/247 163/163 209/213 126/128 263/277 150/152 I16 B 299/327 198/180 221/223 399/419 193/195 168/190 237/247 163/163 211/213 126/128 263/277 150/152 I17 B 273/307 198/180 211/211 397/405 185/195 166/192 251/251 163/163 215/219 130/146 279/281 150/150 I18 B 273/309 198/180 209/209 397/419 195/207 168/168 253/253 163/163 207/219 136/142 287/295 150/150 I19 B 273/309 198/180 211/211 397/419 195/207 168/168 253/253 163/163 207/219 136/142 289/297 150/150 I20 B 271/271 198/180 221/223 397/397 185/209 190/192 249/249 163/163 215/215 130/134 279/281 150/152 I21 B 337/339 198/198 211/211 403/407 209/209 168/190 243/243 163/181 215/219 126/126 261/261 152/152 I22 B 273/309 198/198 209/209 397/401 185/205 190/180 243/249 163/163 207/207 130/130 253/253 148/150 I23 B 273/309 198/198 211/211 397/401 185/205 190/180 243/249 163/163 207/207 130/130 253/297 148/150 I24 B 337/339 198/198 211/211 403/407 187/187 168/190 261/261 163/181 215/219 126/126 261/261 152/152 I25 B 273/309 198/180 221/221 397/407 185/195 166/192 251/251 165/165 219/221 130/146 279/281 150/150 I26 B 273/311 198/180 211/211 397/419 195/207 168/168 253/253 165/165 209/219 136/142 289/297 150/150 I27 B 273/311 198/180 221/221 397/407 195/207 168/168 253/253 165/165 209/219 136/142 287/295 150/150 I28 B 271/273 198/180 221/221 397/397 185/195 166/180 249/249 165/165 209/219 128/130 253/253 150/152 I29 B 273/311 198/198 221/221 397/397 185/205 166/180 249/251 165/165 209/219 130/134 253/281 150/150 I30 B 271/271 198/198 221/221 397/419 193/195 166/168 241/253 165/165 219/219 126/136 253/289 150/150 I31 C 269/315 198/198 211/211 399/399 193/193 198/198 255/255 163/163 213/215 128/134 257/305 150/150 I32 C 269/297 198/198 211/211 403/419 201/201 190/192 251/251 163/163 213/213 136/138 279/293 150/152 I33 D 273/273 180/180 221/221 397/419 199/199 168/192 261/261 165/181 219/221 136/138 263/295 150/152 I34 D 273/273 198/198 221/221 403/415 211/211 190/192 253/253 165/183 219/229 134/136 297/297 150/150 I35 D 267/271 198/180 221/221 403/415 209/209 192/192 245/255 165/183 215/227 128/134 269/295 150/150 I36 D 273/273 198/198 221/221 415/419 209/211 190/192 249/249 165/165 213/219 134/144 275/279 150/152 I37 D 273/273 198/198 221/221 403/415 211/211 190/192 253/253 165/183 219/227 134/136 293/295 150/150 I38 D 267/271 198/180 221/221 403/415 209/209 192/192 245/255 165/183 215/227 128/134 269/295 150/150 I39 E 339/341 198/180 211/211 397/399 191/209 194/194 251/251 165/187 219/221 132/138 279/279 150/152 I40 E 273/273 198/198 221/223 401/401 187/187 168/192 245/249 191/191 213/221 126/134 279/287 150/152 I41 E 325/341 198/198 211/221 399/409 197/197 168/192 261/261 181/185 219/219 130/136 277/303 152/152 I42 E 341/343 198/198 221/221 401/409 197/197 192/192 245/251 187/191 219/221 130/132 275/277 150/156 I43 E 341/343 198/198 221/221 399/409 197/197 192/192 245/251 187/191 219/221 130/132 275/277 150/156 I44 E 275/283 198/198 221/223 415/419 197/197 198/198 237/251 165/183 211/219 114/130 283/293 150/150 I45 E 283/283 198/180 221/221 403/419 197/197 168/168 237/251 165/165 211/211 128/132 279/283 152/152 I46 E 275/275 198/198 221/221 419/419 193/193 168/196 243/251 165/165 215/215 128/136 277/293 150/152 I47 E 275/275 198/198 221/221 419/419 193/193 168/196 243/251 165/165 215/215 128/136 277/293 150/152
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