Calculate Age-related Expression and Heterogeneity Changes for Gene

Calculate Age-related Expression and Heterogeneity Changes for Gene

calc.het.feat(exprs, age, modex = "linear",
  het_change_met = "spearman")

Arguments

exprs

a numeric vector with the expression values, ordered the same as age vector
age

a numeric vector, where the names correspond to samples (the same as colnames of the given matrix).
modex

expression change calculation method. 'linear' or 'loess', defaults to 'linear'
het_change_met

heterogeneity change calculation method. 'LR', for 'linear regression', or and correlation method accepted by cor.test() function.

Value

a list with i) summary results with the effect size and p value for expression level and heterogeneity changes, ii) residuals from expr~age model, which corresponds to unexplained variance, iii) expression values passed into the function.

Examples

myexp <- rnorm(n = 20, mean = sample(1:3, 1), sd = sample(c(1, 3), 1))
agevec <- sample(20:80,20)
het_result <- calc.het.feat(myexp, agevec)
head(het_result$summary) # summary statistics
#>           level_change         level_change.p   heterogeneity_change 
#>            -0.01170475             0.39934927            -0.31578947 
#> heterogeneity_change.p 
#>             0.17475514 
het_result$residuals # heterogeneity values: residuals
#>           1           2           3           4           5           6 
#>  0.73012526  0.30974591 -0.84031662  0.48001273  0.90223371 -0.62179067 
#>           7           8           9          10          11          12 
#> -0.42494927  0.40972535 -0.71218218 -0.05164055  1.33004567 -1.38672970 
#>          13          14          15          16          17          18 
#> -0.98912304 -0.22761943 -0.07869377 -1.38801342  1.81355618 -1.29152474 
#>          19          20 
#>  0.90135427  1.13578429 
het_result$expression  # input expression values
#>  [1] 4.104436 3.426553 2.370128 3.713867 3.855174 2.225807 2.364125 3.163685
#>  [9] 2.580196 2.819367 4.353214 1.659849 1.905294 2.573159 2.921066 1.775612
#> [17] 4.696268 1.907215 3.994752 4.498391
all(myexp == het_result$expression)
#> [1] TRUE