rank.aggregation: Aggregate Rankings

In estfernan/boost: Bayesian Modeling of Spatial Transcriptomics Data

Aggregate Rankings

Description

Generate an aggregated ranking from multiple base rankers.

Usage

rank.aggregation(
  data,
  K,
  method = c("GEO", "MC2"),
  ties.method = c("average", "first", "last", "random", "max", "min")
)

Arguments

data	An n-by-(p+1) numeric matrix that represents a table of p-values with n observations and p+1 variables. Note that the first column should be the gene name and the columns following after should be the methods (i.e., base rankers).
K	A numeric value that indicates how many top-K genes to sort out in each base ranker.
method	A character string that specifies the rank aggregation method.
ties.method	A character string that specifies how ties should be treated (see "Details" in base::rank()).

Details

See Schimek, M. G. et al. (2015) for more information on the procedure.

Value

A numeric matrix that represents a table with genes and their rank.

References

Li, X., Wang, X., & Xiao, G. (2019). A comparative study of rank aggregation methods for partial and top ranked lists in genomic applications. Briefings in bioinformatics, 20(1), 178–189. https://doi.org/10.1093/bib/bbx101.

Schimek M., Budinska E., Kugler K., Svendova V., Ding J., Lin S. (2015). “TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists.” Stat Appl Genet Mol Biol, 311-6. http://www.degruyter.com/doi/10.1515/sagmb-2014-0093.

estfernan/boost documentation built on June 24, 2022, 12:20 a.m.