Rank_overall: Obtaining the overall perturbation effect ranking list.

In BinDuan/MASCOT: Model-based Analysis of Single cell CRISPR knockOuT screening

Description

MASCOT prioritizes the gene knockout effect either as an overall perturbation effect on the cells, or in a functional topic-specific way. Here, the function calcultes and obtains the overall perturbation effect ranking list.

Usage

Rank_overall(distri_diff, offTarget_hash = hash())

Arguments

distri_diff	A dataframe showing the topic distribution difference between case and control which can obtain from "Get_distribution_diff()".
offTarget_hash	A hash table showing offtarget information which can obtain from "Get_Offtarget()". The default is a null hash.

Details

MASCOT obtains the overall perturbation effect ranking list by calculating the distribution difference of the perturbation between case and control as the Jensen-Shannon divergence (JSD). Then the overall knockout efficiency and background difference are calculated and applied to rectify the distribution difference.

Value

rank_overall_result_summary	The overall perturbation effect ranking list with the main information.
rank_overall_result_detail	The overall perturbation effect ranking list with the detailed information.

Author(s)

Bin Duan

References

Hinrich Sch<c3><bc>tze; Christopher D. Manning (1999). Foundations of Statistical Natural Language Processing. Cambridge, Mass: MIT Press. p.304.

BinDuan/MASCOT documentation built on May 23, 2019, 2:42 p.m.