Compute the distance-to-median statistic for the CV2 residuals of all genes
Usage
DM(mean, cv2, win.size=50)
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.
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.
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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(scran)
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/scran/DM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Distance-to-median
> ### Title: Compute the distance-to-median statistic
> ### Aliases: DM
> ### Keywords: variance
>
> ### ** Examples
>
> ngenes <- 10000
> means <- exp(runif(ngenes, 2, 8))
> cv2 <- rgamma(ngenes, 5, 5)
> dm.stat <- DM(means, cv2)
>
>
>
>
>
> dev.off()
null device
1
>