Description Usage Arguments Details Value Author(s) See Also Examples
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).
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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.
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Loading required package: limma
[1] 1000 4
[1] "Sample1" "Sample2" "Sample3" "Sample4"
group lib.size norm.factors
Sample1 1 5180 1
Sample2 1 4977 1
Sample3 2 5220 1
Sample4 2 4912 1
An object of class "DGEList"
$counts
Sample1 Sample2 Sample3 Sample4
1 1 6 0 2
2 4 10 6 1
3 7 6 2 4
4 5 8 0 13
5 3 4 3 7
995 more rows ...
$samples
group lib.size norm.factors
Sample1 1 5180 1
Sample2 1 4977 1
Sample3 2 5220 1
Sample4 2 4912 1
$genes
Symbol
1 Gene1
2 Gene2
3 Gene3
4 Gene4
5 Gene5
995 more rows ...
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