DEswan: Differential Expression - Sliding Window ANalysis (DE-SWAN)

In lehallib/DEswan: Differential Expression Sliding Window ANalaysis

Description

Differential Expression - Sliding Window ANalysis (DE-SWAN)

Usage

DEswan(data.df, qt, window.center, buckets.size, covariates)

Arguments

data.df:	a data Frame - columns are variables and rows are samples (same order as qt and covariates)
qt:	a Vector - quantitative trait for DE-SWAN (same order as data.df and covariates)
window.center:	an optional Vector - window centers. Default is quantile(qt, probs = seq(.1,.9,.1))
buckets.size:	an optional Numeric - size of each bucket. Default is set to (max(range(qt))-min(range(qt)))/2
covariates:	a data Frame. Columns are variables and rows are samples (same order as qt and covariates)

Value

list of 2 data Frames: $p = pvalues of qT and covariates for each variable and each window.center and $coefficients = coefficients of qT and covariates for each variable and each window.center

Examples

res.DEswan=DEswan(data.df = agingplasmaproteome[,-c(1:3)],
               qt = agingplasmaproteome[,1],
               window.center = seq(40,100,10),
               buckets.size = 10,
               covariates = agingplasmaproteome[,c(2:3)])
head(res.DEswan$p)
head(res.DEswan$coeff)

lehallib/DEswan documentation built on Oct. 5, 2020, 9:51 p.m.