DGEList {edgeR} | R Documentation |
Creates a DGEList
object from a table of counts (rows=features, columns=samples), group indicator for each column, library size (optional) and a table of feature annotation (optional).
DGEList(counts = matrix(0, 0, 0), lib.size = colSums(counts), norm.factors = rep(1,ncol(counts)), samples = NULL, group = NULL, genes = NULL, remove.zeros = FALSE)
counts |
numeric matrix of read counts. |
lib.size |
numeric vector giving the total count (sequence depth) for each library. |
norm.factors |
numeric vector of normalization factors that modify the library sizes. |
samples |
data frame containing information for each sample. |
group |
vector or factor giving the experimental group/condition for each sample/library. |
genes |
data frame containing annotation information for each gene. |
remove.zeros |
logical, whether to remove rows that have 0 total count. |
To facilitate programming pipelines,
NULL
values can be input for lib.size
, norm.factors
, samples
or group
, in which case the default value is used as if the argument had been missing.
a DGEList
object
edgeR team. First created by Mark Robinson.
y <- matrix(rnbinom(10000,mu=5,size=2),ncol=4) d <- DGEList(counts=y, group=rep(1:2,each=2)) dim(d) colnames(d) d$samples