todo.org

Todo

Presubmission [6/6]:

Update .rda to new universalmotif

change tomtom pvalue -> pval, etc. to match universalmotif_df format

Change the tomtom_df that gets returned & nested

change the nest_tomtom functions to grab new colnames

Update docs accordingly

view_tomtom_hits %>% cowplot subscript out of bounds error

doesn’t reproduce on my local image, try pulling newest docker image & trying again.

• Candidate issue: https://github.com/wilkelab/cowplot/blame/901173d7a7db61f3e8883944dda8e5181fc2625f/R/plot_grid.R
  • see line ~180

runFimo skip_matched_sequence = TRUE a good default??

Consider swapping to FALSE. This may be a premature optimization.

Double check that runDreme and runMeme docs show correct colnames for return values

runTomTom dist=ed

Make this change before you submit so it’s the default!!

• Change tomtom vignette & tests to ensure correct behavior

Post submission [1/6]:

update example_dreme_tomtom, and example_tomtom after dist=ed

https://bioconductor.org/developers/how-to/git/new-package-workflow/

fix cmdfun::cmd_ui_file_exists

If path = NULL, then when it gets passed to cmd_ui_file_exists(path), get a “path must be character” error.

To fix, catch if path = NULL after if(class(x) == “try-error”) & return FALSE. “` x <- try(path_search(path = path) %>% cmd_ui_file_exists(), silent = TRUE) if (is(x, “try-error”)) { cmd_ui_file_exists(path) return(invisible(NULL)) } “`

TEMPORARY FIX for memes

Trycatch this warning if path == NULL

add bioconductor_docker_meme instructions to install vignette?

update README

Support STREME & ENR

Review [4/7]:

double check all <<- that they’re safe

run bfg to remove >5MB files

reduce function length < 50 lines?

check that view_tomtom_results losing \donttest works

ensure all TODO’s are OK

buff up chip-seq vignette with more text

finish writing the introduction section & early bits about orphan/ectopic binding

• describe experimental setup
• walk through details of each step
• add a `view_motifs` step to the runDreme parts.
  • tell users to check for low quality repetitive DNA, etc.

fix AME Heatmap visualization intro & discussion

ex from matt: “` Using p-value heatmaps to make inter-group comparisons can be useful to visualize differential enrichment of motifs. But such heatmaps can be misleading, particularly when AME produces a very large number of hits… “`

WAIT version bump & push to bioc