More to do fixes

[machlabd]

main fixes:

• vignette: stabsel: in example, set number of PWMs to 200, to also pick up correlated TFs
• calcBinnedMotifEnrR: set NA when motif has zero FG AND BG hits, and print a warning if this happens and verbose.
• vignette: fix when problems occur with NA values (like when selecting motifs with a certain p-value)
• for NA values, set to zero when doing clustering in plotMotifHeatmaps(), and added na_col = "white" as a parameter.
• fix .glmnetRandomizedLasso() documentation.
• make test="fisher" default method.
• general fixes in the vignette, and particularly for the stability selection part, adding a comment on the colinearity problem.

other points:

• should the message of NA values existing be removed, and added as a comment in the help page of the function
• .rds file read into vignette (binned approach) needs to be updated

[codecov[bot]]

Codecov Report

Merging #40 (ffd53d9) into master (af9ed64) will increase coverage by 0.00%. The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master      #40   +/-   ##
=======================================
  Coverage   99.50%   99.50%           
=======================================
  Files          13       13           
  Lines        2019     2036   +17     
=======================================
+ Hits         2009     2026   +17     
  Misses         10       10           

Impacted Files	Coverage Δ
R/stability_selection.R	100.00% <ø> (ø)
R/motif_enrichment_monaLisa.R	100.00% <100.00%> (ø)
R/plotting.R	100.00% <100.00%> (ø)

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