topVar: Table of top-ranked differentially variable CpGs

In ChuanJ/test: Analysing Illumina HumanMethylation BeadChip Data

Description

Extract a table of the top-ranked CpGs from a linear model fit after a differential variability analysis.

Usage

topVar(fit, coef = NULL, number = 10, sort = TRUE)

Arguments

fit	list containing a linear model fit produced by varFit. The fit object should be of class MArrayLM.
coef	column number or column name specifying which coefficient of the linear model fit is of interest. It should be the same coefficient that the differential variability testing was performed on. Default is last column of fit object.
number	maximum number of genes to list. Default is 10.
sort	logical, default is TRUE. Sorts output according the P-value. FALSE will return results in same order as fit object.

Details

This function summarises the results of a differential variability analysis performed with varFit. The p-values from the comparison of interest are adjusted using Benjamini and Hochberg's false discovery rate with the function p.adjust. The top ranked CpGs are selected by first ranking the adjusted p-values, then ranking the raw p-values. At this time no other sorting option is catered for.

Value

Produces a dataframe with rows corresponding to the top CpGs and the following columns:

genelist	one or more columns of annotation for each CpG, if the gene information is available in fit
AvgVar	average of the absolute or squared Levene residuals across all samples
DiffVar	estimate of the difference in the Levene residuals corresponding to the comparison of interest
t	moderated t-statistic
P.Value	raw p-value
Adj.P.Value	adjusted p-value

Author(s)

Belinda Phipson

References

Phipson, B., and Oshlack, A. (2014). A method for detecting differential variability in methylation data shows CpG islands are highly variably methylated in cancers. Genome Biology, 15:465.

Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series, B, 57, 289-300.

See Also

varFit, p.adjust

Examples

# Randomly generate data for a 2 group problem with 100 CpG sites and 5 arrays in each group. 

y<-matrix(rnorm(1000),ncol=10)

group<-factor(rep(c(1,2),each=5))
design<-model.matrix(~group)

# Fit linear model for differential variability
vfit<-varFit(y,design)

# Look at top table of results

topVar(vfit,coef=2)

ChuanJ/test documentation built on Oct. 30, 2019, 5:43 a.m.