mergeSEs: Merge SE objects into single SE object.
In microbiome/mia: Microbiome analysis

mergeSEs

R Documentation

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 = NA,
  collapse_samples = FALSE,
  collapse_features = TRUE,
  verbose = TRUE,
  ...
)

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

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

Arguments

`x`	a `SummarizedExperiment` object or a list of `SummarizedExperiment` objects.
`...`	optional arguments (not used).
`assay.type`	A character value for selecting the `assay` to be merged. (By default: `assay.type = "counts"`)
`assay_name`	(Deprecated) alias for `assay.type`.
`join`	A single character 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. (By default: `join = "full"`)
`missing_values`	NA, 0, or a single character values specifying the notation of missing values. (By default: `missing_values = NA`)
`collapse_samples`	A boolean value for selecting whether to collapse identically named samples to one. (By default: `collapse_samples = FALSE`)
`collapse_features`	A boolean value for selecting 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. (By default: `collapse_features = TRUE`)
`verbose`	A single boolean value to choose whether to show messages. (By default: `verbose = 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_samples = 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.

Author(s)

Leo Lahti and Tuomas Borman. Contact: microbiome.github.io

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_samples'
tse_temp <- mergeSEs(list(tse[1:10, 1], tse[1:20, 1], tse[1:5, 1]), 
                       collapse_samples = 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 April 27, 2024, 4:04 a.m.