voom_weights: Precision weights accounting for heteroscedasticity in...

In tcgsaseq: Time-Course Gene Set Analysis for RNA-Seq Data

Description

Implementation of the procedure described in Law et al. for estimating precision weights from RNA-seq data.

Usage

voom_weights(
  y,
  x,
  preprocessed = FALSE,
  doPlot = FALSE,
  lowess_span = 0.5,
  R = NULL
)

Arguments

y	a matrix of size G x n containing the raw RNA-seq counts or preprocessed expressions from n samples for G genes.
x	a matrix of size n x p containing the model covariates from n samples (design matrix).
preprocessed	a logical flag indicating whether the expression data have already been preprocessed (e.g. log2 transformed). Default is FALSE, in which case y is assumed to contain raw counts and is normalized into log(counts) per million.
doPlot	a logical flag indicating whether the mean-variance plot should be drawn. Default is FALSE.
lowess_span	smoother span for the lowess function, between 0 and 1. This gives the proportion of points in the plot which influence the smooth at each value. Larger values give more smoothness. Default is 0.5.
R	library.size (optional, important to provide if preprocessed = TRUE). Default is NULL

Value

a vector of length n containing the computed precision weights

References

Law, C. W., Chen, Y., Shi, W., & Smyth, G. K. (2014). voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology, 15(2), R29.

See Also

lowess approxfun voom

Examples

#rm(list=ls())
set.seed(123)

G <- 10000
n <- 12
p <- 2

y <- sapply(1:n, FUN=function(x){rnbinom(n=G, size=0.07, mu=200)})
x <- sapply(1:p, FUN=function(x){rnorm(n=n, mean=n, sd=1)})

my_w <-  voom_weights(y, x, doPlot=TRUE)
if (requireNamespace("limma", quietly = TRUE)) {
 w_voom <- limma::voom(counts=y, design=x, plot=TRUE) #slightly faster - same results
 all.equal(my_w, w_voom$weights)
}

## Not run: 
microbenchmark::microbenchmark(limma::voom(counts=t(y), design=x, plot=FALSE),
                              voom_weights(x, y, doPlot=FALSE), times=30)
## End(Not run)

tcgsaseq documentation built on Sept. 13, 2020, 5:13 p.m.