Error: object 'tri' not found in getTriFromFasta

[ipstone]

Hello,

thank you for the pointer in raerose01/deconstructSigs#20 regarding the scaling factor calculation. I am trying it on BALBC fasta file, but got the following error:

[1] "Processing - BALBC"
Error: object 'tri' not found

Where is the tri object from, in this function? https://github.com/nriddiford/mutationProfiles/blob/master/R/triCount.R

Thanks a lot! Below are some additional details:

In addition: Warning message:
data_frame() is deprecated, use tibble().
This warning is displayed once per session.

traceback()
18: mutate_impl(.data, dots, caller_env())
17: mutate.tbl_df(tbl_df(.data), ...)
16: mutate(tbl_df(.data), ...)
15: as.data.frame(mutate(tbl_df(.data), ...))
14: mutate.data.frame(., genome_adj = tri * 2)
13: mutate(., genome_adj = tri * 2)
12: function_list[i]
11: freduce(value, _function_list)
10: _fseq(_lhs)
9: eval(quote(_fseq(_lhs)), env, env)
8: eval(quote(_fseq(_lhs)), env, env)
7: withVisible(eval(quote(_fseq(_lhs)), env, env))
6: triCount %>% data.frame() %>% mutate(genome_adj = tri * 2) %>%
mutate(x = 1/tri) %>% select(x) at calc_trinucleotide_scaling_factor.R#76
5
: getTriFromFasta("/GATKBundle/reference/M_musculus/assembly/BALBC/BALBC_genome.fa") at calc_trinucleotide_scaling_factor.R#87
4: eval(ei, envir)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("calc_trinucleotide_scaling_factor.R")