Merge SummarizedExperiment objects together — merge

Merges two or more SummarizedExperiment objects together. Can be used to merge analytical modes or batches.

Usage

merge_objects(..., merge = c("features", "samples"), assay.type = NULL)

Arguments

...: SummarizedExperiment objects or a list of objects
merge: what to merge? features is used for combining analytical modes, samples is used for batches
assay.type: character, assay to be used in case of multiple assays. The same assay needs to be present in all objects to be merged, and the resultant object contains this single assay.

Value

A merged SummarizedExperiment object.

Details

When merging samples, sample IDs that begin with "QC" or "Ref" are combined so that they have running numbers on them. This means that if both batches have samples called "QC_1", this will not result in an error, but the sample IDs will be adjusted so that they are unique.

Examples

# Merge analytical modes
data(hilic_neg_sample, hilic_pos_sample, rp_neg_sample, rp_pos_sample)
merged <- merge_objects(
  hilic_neg_sample, hilic_pos_sample,
  rp_neg_sample, rp_pos_sample
)
# Merge batches
batch1 <- example_set[, example_set$Batch == 1]
batch2 <- example_set[, example_set$Batch == 2]
merged <- merge_objects(batch1, batch2, merge = "samples")