About the always.selected parameter problem

[hungweichen0327]

Dear community,

I use the example data from the corehunter package in R and I tried to use always.selected function. Unfortunately, I failed to select particular IDs I want. Can you help me to fix the problem? Thank you!

The code I ran in R as below:

library (corehunter)

dist.file <- system.file ("extdata", "distances.csv", package = "corehunter")
my.data <- distances (file = dist.file)

core.test <- sampleCore(my.fasta, always.selected = integer(1))
core.test2 <- sampleCore(my.fasta, always.selected = character("Bred_0003"))

After I ran the code:
core.test <- sampleCore(my.fasta, always.selected = integer(1))
or
core.test2 <- sampleCore(my.fasta, always.selected = character("Bred_0003"))

The message showed:

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  :
  java.lang.IllegalArgumentException: Error while creating subset solution: set of selected IDs should be a subset of set of all IDs.

I see the issue now. always.selected needs to be a vector. So please try the following if you always want to include the first accession.

core.test <- sampleCore(my.data, always.selected = c(1))

For the other fixed indices, simply specify them by index eg.

core.test <- sampleCore(my.data, always.selected = c(1, 3))

Please can you confirm this works for you, and I will close the issue?

[hungweichen0327]

Thank you for the reply. Do you mean that I can not use a vector including particular ID for the always.selected parameter? The value that always.selected parameter can detect is only the integer/number, not the character/ID.

I am not really sure why this does not work

core.test2 <- sampleCore(my.data, always.selected = c("Bred_0003"))

[hungweichen0327]

Dear Dr. Davenport,

The previous code you suggested can run:

core.test <- sampleCore(my.data, always.selected = c(1))

I also don't know why it's doesn't work about this code:

core.test2 <- sampleCore(my.data, always.selected = c("Bred_0003"))

I will have a look again at the weekend. Looking at the code it should work.

[hungweichen0327]

Thank you for the help.