mergeSEs: Merge SE objects into single SE object.

In microbiome/mia: Microbiome analysis

Merge SE objects into single SE object.

Description

Merge SE objects into single SE object.

Usage

mergeSEs(x, ...)

## S4 method for signature 'SimpleList'
mergeSEs(
  x,
  assay.type = "counts",
  assay_name = NULL,
  join = "full",
  missing.values = missing_values,
  missing_values = NA,
  collapse.cols = collapse_samples,
  collapse_samples = FALSE,
  collapse.rows = collapse_features,
  collapse_features = TRUE,
  verbose = TRUE,
  ...
)

## S4 method for signature 'SummarizedExperiment'
mergeSEs(x, y = NULL, ...)

## S4 method for signature 'list'
mergeSEs(x, ...)

Arguments

x	TreeSummarizedExperiment.
...	optional arguments (not used).
assay.type	Character scalar. Specifies which assay to use for calculation. (Default: "counts")
assay_name	Deprecated. Use assay.type instead.
join	Character scalar. A value for selecting the joining method. Must be 'full', 'inner', 'left', or 'right'. 'left' and 'right' are disabled when more than two objects are being merged. (Default: "full")
missing.values	NA, 0 or Character scalar. Specifies the notation of missing values. (By default: NA)
missing_values	Deprecated. Use missing.values instead.
collapse.cols	Logical scalar. Determines whether to collapse identically named samples to one. (Default: FALSE)
collapse_samples	Deprecated. Use collapse.cols instead.
collapse.rows	Logical scalar. Selects whether to collapse identically named features to one. Since all taxonomy information is taken into account, this concerns rownames-level (usually strain level) comparison. Often OTU or ASV level is just an arbitrary number series from sequencing machine meaning that the OTU information is not comparable between studies. With this option, it is possible to specify whether these strains are combined if their taxonomy information along with OTU number matches. (Default: TRUE)
collapse_features	Deprecated. Use collapse.rows instead.
verbose	Logical scalar. Choose whether to show messages. (Default: TRUE)
y	a SummarizedExperiment object when x is a SummarizedExperiment object. Disabled when x is a list.

Details

This function merges multiple SummarizedExperiment objects. It combines rowData, assays, and colData so that the output includes each unique row and column ones. The merging is done based on rownames and colnames. rowTree and colTree are preserved if linkage between rows/cols and the tree is found.

Equally named rows are interpreted as equal. Further matching based on rowData is not done. For samples, collapsing is disabled by default meaning that equally named samples that are stored in different objects are interpreted as unique. Collapsing can be enabled with collapse.cols = TRUE when equally named samples describe the same sample.

If, for example, all rows are not shared with individual objects, there are missing values in assays. The notation of missing can be specified with the missing.values argument. If input consists of TreeSummarizedExperiment objects, also rowTree, colTree, and referenceSeq are preserved if possible. The data is preserved if all the rows or columns can be found from it.

Compared to cbind and rbind mergeSEs allows more freely merging since cbind and rbind expect that rows and columns are matching, respectively.

You can choose joining methods from 'full', 'inner', 'left', and 'right'. In all the methods, all the samples are included in the result object. However, with different methods, it is possible to choose which rows are included.

• full – all unique features

• inner – all shared features

• left – all the features of the first object

• right – all the features of the second object

The output depends on the input. If the input contains SummarizedExperiment object, then the output will be SummarizedExperiment. When all the input objects belong to TreeSummarizedExperiment, the output will be TreeSummarizedExperiment.

Value

A single SummarizedExperiment object.

See Also

• TreeSummarizedExperiment::cbind

• TreeSummarizedExperiment::rbind

• full_join

• inner_join

• left_join

• right_join

Examples

data(GlobalPatterns)
data(esophagus)
data(enterotype)

# Take only subsets so that it wont take so long
tse1 <- GlobalPatterns[1:100, ]
tse2 <- esophagus
tse3 <- enterotype[1:100, ]

# Merge two TreeSEs
tse <- mergeSEs(tse1, tse2)

# Merge a list of TreeSEs
list <- SimpleList(tse1, tse2, tse3)
tse <- mergeSEs(list, assay.type = "counts", missing.values = 0)
tse

# With 'join', it is possible to specify the merging method. Subsets are used
# here just to show the functionality
tse_temp <- mergeSEs(tse[1:10, 1:10], tse[5:100, 11:20], join = "left")
tse_temp

# If your objects contain samples that describe one and same sample,
# you can collapse equally named samples to one by specifying 'collapse.cols'
tse_temp <- mergeSEs(list(tse[1:10, 1], tse[1:20, 1], tse[1:5, 1]), 
                       collapse.cols = TRUE,
                       join = "inner")
tse_temp

# Merge all available assays
tse <- transformAssay(tse, method="relabundance")
ts1 <- transformAssay(tse1, method="relabundance")
tse_temp <- mergeSEs(tse, tse1, assay.type = assayNames(tse))

microbiome/mia documentation built on Nov. 20, 2024, 1:12 a.m.