identifyBestGrouping-methods: description of function identifyBestGrouping

In stela2502/StefansExpressionSet: StefansExpressionSet

description of function identifyBestGrouping

Description

This function compares several groupings to each other.

In addition the groupings are combined in a way, that if a sample end up in group 1 in grouing A but in group 2 in groupung B

it might be something else than a sample ending up in group 1 for both.

The quality of the groupings will be accessed in two stated (1) there should not be too many small groups and

(2) the genes should be differentially expressed in these groups. The differential expression is accessed

using a straight forward anova approach (excluding the not called genes for a SingleCellsNGS object).

Usage

identifyBestGrouping(x, groups, namePrefix = "identifyBestGrouping",
  cut = 0.05)

Arguments

x	the SingleCellsNGS
groups	the colnames (samples) that contain the grouping information (default)
namePrefix	a common name prefix for this analysis
cut	define the p value cut off for the test ( if too view signfican genes are detected at 0.05)

Value

A list containing the number of significant genes in each possible combination of groups and the SingleCellsNGS object containg all annotations and stats.

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