add flowclean for QC in default pipeline (on wiki?)

[FMKerckhof]

Recently, we saw with the Accuri that in high-throuphut experiments there could occur missed issues on stability of the data. Could we implement a standardized check? We already (briefly) evaluated flowClean (http://bioconductor.org/packages/release/bioc/html/flowClean.html), however it appears to be quite slow.

Suggestions:

• We develop our own autocorrelation-based approach
• We optimize the flowClean code and include it here

[rprops]

It is unclear to me how flowClean adjusts the volume measured based on the events removed? Removing spurious and erroneous measurements is a good thing for the diversity assessment but will bias the counts. I'll try to evaluate it on the test data set and try to incorporate it into the Diversity_rf and beta_div_fcm functions as an additional option.

[FMKerckhof]

if you'd need to evaluate/validate it with test data, say a defined concentration of peak beads, I could create the required FCS files with the FACSVerse or the C6

[rprops]

I've implemented the flowClean function in the Diversity_rf function and tested in on the test data (flowData) but it did not detect any outliers. Will update wiki.

[rprops]

Wiki is updated for alpha div. Will update beta div function to offer the same functionality.

[rprops]

Have adjusted wiki - so everything should be good to go.

[FMKerckhof]

However, for sure with the latest release, the flowAI bioconductor package is probably the better option.