Average Assays Across Replicates

This function takes a list of SummarizedExperiment objects. It averages the requested assay between all input objects and returns a new single SummarizedExperiment object with the averaged assay.

averageReplicates(list, assay.type = "matrix")

Arguments

list	A list of SummarizedExperiment objects.
assay.type	Name the assay to average between all samples.

Value

A SummarizedExperiment object with the averaged assay.

Examples

# Prepare example data ----

sample_names <- c("A", "B", "C")

se_list <- generateDeeptoolsExperiments(20, 10, sample_names)
se_list
#> $A
#> class: RangedSummarizedExperiment 
#> dim: 20 10 
#> metadata(0):
#> assays(1): matrix
#> rownames(20): GR_1 GR_2 ... GR_19 GR_20
#> rowData names(0):
#> colnames(10): 1 2 ... 9 10
#> colData names(0):
#> 
#> $B
#> class: RangedSummarizedExperiment 
#> dim: 20 10 
#> metadata(0):
#> assays(1): matrix
#> rownames(20): GR_1 GR_2 ... GR_19 GR_20
#> rowData names(0):
#> colnames(10): 1 2 ... 9 10
#> colData names(0):
#> 
#> $C
#> class: RangedSummarizedExperiment 
#> dim: 20 10 
#> metadata(0):
#> assays(1): matrix
#> rownames(20): GR_1 GR_2 ... GR_19 GR_20
#> rowData names(0):
#> colnames(10): 1 2 ... 9 10
#> colData names(0):
#> 

# Usage ----

averageReplicates(se_list)
#> class: RangedSummarizedExperiment 
#> dim: 20 10 
#> metadata(0):
#> assays(1): matrix
#> rownames(20): GR_1 GR_2 ... GR_19 GR_20
#> rowData names(0):
#> colnames(10): 1 2 ... 9 10
#> colData names(0):