topTrendy: obtain top genes from trendy results
In rhondabacher/Trendy: Breakpoint analysis of time-course expression data

topTrendy

R Documentation

obtain top genes from trendy results

Description

reformats the list output for genes with a given adjusted R^2 cutoff

Usage

topTrendy(trendyOutData, adjR2Cut = 0.5)

Arguments

`trendyOutData`	output from the trendy function
`adjR2Cut`	cutoff for the adjusted R^2. Genes whose adjusted R^2 is greater than adjR2Cut are called as significant.

Value

only significant genes will be included in the output. The output is reformatted as: Trend direction of each sample; -1: down, 0: no change, 1: up Slope: fitted slopes, Slope.Trend: sign of fitted slopes, Slope.Pvalue: p value of each segment, Breakpoint: estimated breakpoints, Fitted.Values: fitted values AdjustedR2: adjusted r value of the model Fit: fit object

Examples

 d1 <- matrix(c(c(rnorm(50,5,1),sort(rnorm(50, 15, 5))), rnorm(100, 50,10)), 2, 100, TRUE)
 rownames(d1) <- c("g1","g2")
 colnames(d1) <- paste0("time", seq_len(100))
 seg.all <- trendy(d1)
 seg.all <- results(seg.all)
 top.genes <- topTrendy(seg.all)

rhondabacher/Trendy documentation built on Oct. 26, 2023, 3:46 a.m.