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I am curious, all the global variables in this script must've generated an error with devtools:check() since none of them are documented.

I recently added some variables in this style to GAMBLR.data and the check command complained that the documentation for such variables was missing.

So I am just curious if we're aware of this "error" in this package, or if there's something else going on.

The following functions are currently missing documentation:

• bins_to_bedgraph.R
• cache_output.R
• check_file_details.R
• compare_coding_mutation_pattern.R
• copy_no_clobber.R
• gene_mutation_tally.R
• get_template_wildcards.R
• get_unmatched_normals.R
• grob_wildcards.R
• socketWrite.R
• test_glue.R
• web_add_update_page.R

Ensure function import tags and in-code package prefixing are constant and up to date. Issue added for tracking purposes.

From a comment by Vladimir in PR Fixing internal call of get_sample_cn_segments in examples #17

I think this subset_cnstates function could be tweaked in the future. When run, it creates some objects in the global environment.

> rm(list=ls())
> devtools::load_all("/home/vsouza/repos/gamblr_repos/test_branches/GAMBLR.helpers/pr17/GAMBLR.helpers")
> cn_states = get_sample_cn_segments(these_sample_ids = c("02-13135T",
+                                                         "SU-DHL-4"),
+                                    streamlined = FALSE)
> ls()
[1] "cn_states"
> subset_cnstates(cn_segments = cn_states,
+                 samplen = 1)
> ls()
[1] "cn_1_sample1" "cn_3_sample1" "cn_4_sample1" "cn_5_sample1" "cn_6_sample1" "cn_states"   

As a consequence, when we run fancy_multisamp_ideogram, which internally runs subset_cnstates, these objects are also created in the global env, which probably is not a desirable but weird behaviour.

> rm(list=ls())
> library(GAMBLR.viz)
> fancy_multisamp_ideogram(these_sample_ids = c("05-18426T", "05-18426T"),
+                          include_cn2 = TRUE,
+                          plot_title = "Multi-sample Ideograms Example",
+                          plot_sub = "grch37",
+                          chr_anno_dist = 2.5,
+                          chr_select = paste0("chr", c(1:22)))
> ls()
[1] "cn_0_sample1" "cn_1_sample1" "cn_2_sample1" "cn_3_sample1" "cn_4_sample1"

If this is important, I could change it to not leave these "leftover" objects, or maybe just create an issue. What do you think?

The main README of this package should eventually be updated to provide more information on how to use this package and for what purpose this package was developed in the first place. Maybe the READMEs of all GAMBLR thematic packages should be standardized in a way that makes everything look uniform, to a certain extent.