extractPattern: Extract pattern from segmented regression

In Trendy: Breakpoint analysis of time-course expression data

Description

find dynamic genes that follow a given pattern

Usage

extractPattern(trendyOutData, Pattern = NULL, adjR2Cut = 0.5,
  Delay = 0)

Arguments

trendyOutData	output from trendy() function
Pattern	vector containing pattern to search genes/features (e.g, c("up", "down")), no-change is designated by "same". If length is one (e.g c("up")) then it will only consider features with constant pattern across the entire time-course.
adjR2Cut	only consider features with adjusted R^2 > adjR2Cut. Default = .5.
Delay	search for pattern starting after certain time-point (e.g. only genes with a breakpoint > 10).

Value

Genes: names of genes/features containing pattern and the breakpoints corresponding to the pattern.

Author(s)

Rhonda Bacher

Examples

 myTrends <- trendy(trendyExampleData[seq_len(5),], tVect=seq_len(40))
 myTrends <- results(myTrends)
 #extractPattern(myTrends, Pattern = c("up")) #increasing only features
 #extractPattern(myTrends, Pattern = c("same", "down")) 
 #extractPattern(myTrends, Pattern = c("up", "down"), Delay = 20)

Trendy documentation built on Nov. 8, 2020, 8:10 p.m.