maf_to_custom_track returns error

[vladimirsouza]

maf_to_custom_track returns the following error:

Error: 'get_ash' is not an exported object from 'namespace:ggsci'

Here is an example to reproduce the error:

library(GAMBLR)
library(tidyverse)

#set sample ID
this_sample = "00-15201_tumorA"

#get_ssm_by_sample
this_sample_ssm = get_ssm_by_sample(this_sample_id = this_sample, 
                                    this_seq_type = "genome",
                                    projection = "grch37")

#annotate mutational hotspots
this_sample_ssm_hot = annotate_hotspots(mutation_maf = this_sample_ssm, 
                                        recurrence_min = 5,
                                        p_thresh = 0.05,
                                        analysis_base = c("FL--DLBCL"))

#review hotspots
this_sample_ssm_hot_rev = review_hotspots(annotated_maf = this_sample_ssm_hot, 
                                          genes_of_interest = "MYD88", 
                                          genome_build = "grch37")

identical(this_sample_ssm_hot, this_sample_ssm_hot_rev) # They are the same!

#transform the annotated maf into a custom track for UCSC genome browser interrogation
ucsc_customtrack = maf_to_custom_track(maf_data = this_sample_ssm_hot_rev,
                                       as_bigbed = FALSE,
                                       as_biglolly = FALSE,
                                       output_file = "this_sample_custom_track.bed",
                                       track_name = "GAMBL Mutations",
                                       track_description = "Mutations from GAMBL")

My ggsci version:

> packageVersion("ggsci")
[1] ‘3.0.0’

maf_to_custom_track uses get_gambl_colours internally, which in turn uses ggsci::get_ash. However, get_ash is in ggsci v2.9 but no longer in ggsci v3.0.0, which is the newest.

[rdmorin]

This is because you have to install our forked version of ggsci from the Morin lab GitHub repository.

[vladimirsouza]

Thank you. I installed the forked version of ggsci and maf_to_custom_track is working fine now.