DM: Compute the distance-to-median statistic

In scran: Methods for Single-Cell RNA-Seq Data Analysis

Description

Compute the distance-to-median statistic for the CV2 residuals of all genes

Usage

DM(mean, cv2, win.size=51)

Arguments

mean	A numeric vector of average counts for each gene.
cv2	A numeric vector of squared coefficients of variation for each gene.
win.size	An integer scalar specifying the window size for median-based smoothing. This should be odd or will be incremented by 1.

Details

This function will compute the distance-to-median (DM) statistic described by Kolodziejczyk et al. (2015). Briefly, a median-based trend is fitted to the log-transformed cv2 against the log-transformed mean using runmed. The DM is defined as the residual from the trend for each gene. This statistic is a measure of the relative variability of each gene, after accounting for the empirical mean-variance relationship. Highly variable genes can then be identified as those with high DM values.

Value

A numeric vector of DM statistics for all genes.

Author(s)

Jong Kyoung Kim, with modifications by Aaron Lun

References

Kolodziejczyk AA, Kim JK, Tsang JCH et al. (2015). Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation. Cell Stem Cell 17(4), 471–85.

Examples

# Mocking up some data
ngenes <- 1000
ncells <- 100
gene.means <- 2^runif(ngenes, 0, 10)
dispersions <- 1/gene.means + 0.2
counts <- matrix(rnbinom(ngenes*ncells, mu=gene.means, size=1/dispersions), nrow=ngenes)

# Computing the DM.
means <- rowMeans(counts)
cv2 <- apply(counts, 1, var)/means^2
dm.stat <- DM(means, cv2)
head(dm.stat)

Example output

Loading required package: BiocParallel
Loading required package: scater
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2

Attaching package: 'scater'

The following object is masked from 'package:stats':

    filter

Warning message:
In zoo(x = y, order.by = x) :
  some methods for "zoo" objects do not work if the index entries in 'order.by' are not unique
[1] -0.05065798 -0.06376366 -0.02115419  0.03757197  0.11239291 -0.01195606

scran documentation built on April 17, 2021, 6:09 p.m.