topTrendy {Trendy}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 <- rbind(c(rep(1,50),seq_len(50)), rev(seq_len(100)))
 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)

[Package Trendy version 1.6.0 Index]