rfCluster_row: rfCluster_row

rfCluster_rowR Documentation

rfCluster_row

Description

This fucntion uses the RFclust.SGE to create fandomForest based unsupervised clusters on a subset of the data.

Default is on 200 cells using all (provided) genes with 500 forests and 500 trees per forest for 5 repetitions.

You are asked to give a k numer of expected clusters (better too many than too little), classifies the total

data using the 5 different unsupervised runs and all cluster ids from these runs are merged into the final cluster id.

This <summaryCol> will be part of the return objects samples table, together with a <usefulCol> where

all clusters with less than 10 cells have been merged into the 'gr. 0'.

The final results will be reported as new columns in the samples table containing the 'name'

Usage

rfCluster_row(x, rep = 5, SGE = F, email, k = 16, slice = 30,
  subset = 200, nforest = 500, ntree = 500, name = "RFclust",
  settings = list())

Arguments

x

the single cells ngs object

rep

how many repetitions for the random forest grouping should be run (default = 5)

SGE

whether to use the sun grid engine to calculate the rf grouping

email

your email to use together with the SGE option

k

the numer of expected clusters (metter more than to view)

slice

how many processes should be started for each random forest clustering (default = 30)

subset

how many cells should be randomly selected for the unsupervised clustering (default = 200)

nforest

the numer of forests to grow for each rep (defualt = 500)

ntree

the numer of trees per forest (default = 500)

name

if you want to run multiple RFclusterings on e.g. using different input genes you need to specify a name (default ='RFclust')

settings

a list of slurm settings (A t and p are used) that will make the RFclust.SGE module use a slurm backend for calculations.

bestColname

the column name to store the results in

Value

a SingleCellsNGS object including the results and storing the RF object in the usedObj list (bestColname)


stela2502/StefansExpressionSet documentation built on April 24, 2023, 8:15 p.m.