auto_order_grouping-methods: Auto re-order a (RF) grouping

In stela2502/BioData: The package allows to annotate a numeric data.table with col and row data

Description

This function uses the rfCluster_col function to order median collapsed data values. This RF order is then re-ordered twice using hclust 'ward.D2' and the final ordering is forced onto the original grouping.

Usage

auto_order_grouping(
  x,
  group,
  settings = list(A = "lsens2017-3-2", t = "01:00:00", p = "dell", n = 1, N = 1),
  k = 5,
  colapseBy = "median"
)

Arguments

x	The BioData object
group	the sample grouping that should become reordered (min 15 groups)
settings	a list of slurm settings default list( 'A' = 'lsens2017-3-2' , 't'= '01:00:00', 'p' = 'dell', 'n' = 1, 'N' = 1)
k	how many groups to put into one super group (default 5)
colapseBy	which method to collapse the data by (default 'median') see function collaps

stela2502/BioData documentation built on Feb. 23, 2022, 5:47 a.m.