Error in xj[i] : only 0's may be mixed with negative subscripts

Question 1: hard to say for sure without knowing what is in data (please consider making a reprex), but it comes from using [ to select:

# let's create an example vector x
x <- 10:15

# you can use positive indexes to select one or several values
#> [1] 11 13

# you can use negative values to exclude these (and keep everything else)
x[ - c(2,4)]
#> [1] 10 12 14 15

# mixing the two is meaningless: do you want to keep or exclude the ones that are not mentioned?
x[c( -1, 3)]
#> Error in x[c(-1, 3)] : only 0's may be mixed with negative subscripts

more explanations here

So in your function, somehow there is a combination of i and n where c((i-n):(i+n-1)) contains both positive and negative values, R can't guess what you want to do.

Question 2: looks like data is not a data.frame, according to the error message. It works for me:

wtMedian <- function(data){
  chr <- unique(data$chromosome)

my_data <- data.frame(chromosome = c("I","II"),
                       bla = 1:2)
#> [1] "I"  "II"

Created on 2021-11-17 by the reprex package (v2.0.1)