In [1]:

    

library()


    

In [4]:

    

library(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, 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

In [2]:

    

## ---- echo=FALSE, results="hide", message=FALSE--------------------------
require(knitr)
opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)

## ----style, echo=FALSE, results='asis'-----------------------------------
BiocStyle::markdown()

## ----setup, echo=FALSE, message=FALSE------------------------------------
library(scran)
set.seed(100)

## ------------------------------------------------------------------------
ngenes <- 10000
ncells <- 200
mu <- 2^runif(ngenes, 3, 10)
gene.counts <- matrix(rnbinom(ngenes*ncells, mu=mu, size=2), nrow=ngenes)

## ------------------------------------------------------------------------
library(org.Mm.eg.db)
all.ensembl <- unique(toTable(org.Mm.egENSEMBL)$ensembl_id)
rownames(gene.counts) <- sample(all.ensembl, ngenes)

## ------------------------------------------------------------------------
nspikes <- 100
ncells <- 200
mu <- 2^runif(nspikes, 3, 10)
spike.counts <- matrix(rnbinom(nspikes*ncells, mu=mu, size=2), nrow=nspikes)
rownames(spike.counts) <- paste0("ERCC-", seq_len(nspikes))
all.counts <- rbind(gene.counts, spike.counts)

## ------------------------------------------------------------------------
library(scran)
sce <- new


    

    




Loading required package: knitr
Warning message in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
"there is no package called 'knitr'"





    




Error in eval(expr, envir, enclos): object 'opts_chunk' not found
Traceback:

In [3]:

    

library(scran)


    

    




Error in library(scran): there is no package called 'scran'
Traceback:

1. library(scran)
2. stop(txt, domain = NA)

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