AOV1way: One-Way ANOVA

In axm323/dataVisEasy: datavisEasy: Data visualizations Using Annotations Made Easy

One-Way ANOVA

Description

A one-way ANOVA for the samples in the supplied data matrix based on annotations stored in the params list object.

Usage

AOV1way(data.to.aov, category, pthreshold = 0.05, additional.report = "NONE")

Arguments

data.to.aov	numeric data matrix with samples/observations in the columns and genes/variables in the rows
category	Character string pointing to a column of the annotations data frame stores in params$annotations
pthreshold	pvalue threshold for which genes will be considered significant
additional.report	Option to include full output of aov or TukeyHSD, options are "NONE", "AOV","TUKEY", or "ALL"

Details

Runs a standard one-way ANOVA and subsequent TukeyHSD on the data provided using stored annotations as the categories for ANOVA groupings

Value

~List object

AOV.Results	dataframe giving the F statistic and pvalue of each gene in the original input matrix
Sig.Genes	character vector of the genes with pvalues below the specified pthreshold
NonSig.Genes	character vector of the genes with pvalues that did not pass the specified pthreshold
Tukey.pVals	dataframe containing the adjusted pvalues from TukeyHSD for each contrast for each gene in the original input matrix
Tukey.diffs	dataframe containing the difference values from TukeyHSD for each contrast for each gene in the original input matrix

optional items

AOV.output	list object containing the aov output for all genes in the original input matrix
Tukey.output	list object containing the TUkeyHSD output for all genes in the original input matrix

Note

The function itself determines significant and non-significant genes based on the pthreshold provided. However, the AOV.Results provdied in the output supply the F value and p value, additional information can also be retrieved by setting additional report = TRUE, user can use any of this information for custom filtering of results.

For cases where there are no non-missing arguments for one or more of the groups in the supplied categories, a warning will be generated indicating which genes or observations this is true for. If there is only one group with no non-missing arguments, that gene or observation will be removed from the analysis (and will be indicated with a warning). Please pay attention to these warnings as they may affect how the results should be interpretted.

Author(s)

~~Alison Moss~~

Examples

##initiate parameteres and set up annotations

initiate_params()
data(RAGP_norm)
data(RAGP_annots)
set_annotations(RAGP_annots)

##AOV for Connectivity
state.aov <- AOV1way(RAGP_norm, "State")
head(state.aov$AOV.Results)
head(state.aov$Sig.Genes)

##visualize significant genes in heatmap
set_annot_samps("State")
myHeatmapByAnnotation(RAGP_norm, state.aov$Sig.Genes, groupings = "State")


##AOV for Animal
animal.aov <- AOV1way(RAGP_norm, "Animal", pthreshold = 0.01)
summary(animal.aov)
head(animal.aov$Tukey.pVals) ##look at pvalues from tukey post hoc analysis

axm323/dataVisEasy documentation built on Feb. 1, 2024, 11:53 p.m.