Differential Expression - Sliding Window ANalysis (DE-SWAN)

Differential Expression - Sliding Window ANalysis (DE-SWAN)

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)])
#> [1] "window.center  1/7"
#> [1] "window.center  2/7"
#> [1] "window.center  3/7"
#> [1] "window.center  4/7"
#> [1] "window.center  5/7"
#> [1] "window.center  6/7"
#> [1] "window.center  7/7"
head(res.DEswan$p)
#>    variable window.center factor      pvalue
#> 1 Feature_1            40     qt 0.479188190
#> 2 Feature_1            40    Sex 0.064129958
#> 3 Feature_1            40 Cohort 0.002082943
#> 4 Feature_2            40     qt 0.818757036
#> 5 Feature_2            40    Sex 0.106665375
#> 6 Feature_2            40 Cohort 0.116499806
head(res.DEswan$coeff)
#>                           variable window.center        factor  coefficient
#> (Intercept)              Feature_1            40   (Intercept)  3.482908497
#> qt.tmp1                  Feature_1            40            qt  0.035679739
#> covariates$SexMale       Feature_1            40       SexMale  0.103411765
#> covariates$CohortSeattle Feature_1            40 CohortSeattle -0.310418301
#> (Intercept)1             Feature_2            40   (Intercept)  2.723666667
#> qt.tmp11                 Feature_2            40            qt -0.006666667