meltSE: Converting a 'SummarizedExperiment' object into a long...
In FelixErnst/mia: Microbiome analysis

meltSE

R Documentation

Converting a `SummarizedExperiment` object into a long data.frame

Description

meltSE Converts a SummarizedExperiment object into a long data.frame which can be used for tidyverse-tools.

Usage

meltSE(
  x,
  assay.type = assay_name,
  assay_name = "counts",
  add.row = add_row_data,
  add_row_data = NULL,
  add.col = add_col_data,
  add_col_data = NULL,
  row.name = feature_name,
  feature_name = "FeatureID",
  col.name = sample_name,
  sample_name = "SampleID",
  ...
)

## S4 method for signature 'SummarizedExperiment'
meltSE(
  x,
  assay.type = assay_name,
  assay_name = "counts",
  add.row = add_row_data,
  add_row_data = NULL,
  add.col = add_col_data,
  add_col_data = NULL,
  row.name = feature_name,
  feature_name = "FeatureID",
  col.name = sample_name,
  sample_name = "SampleID",
  ...
)

Arguments

`x`	A numeric matrix or a `SummarizedExperiment`
`assay.type`	a `character` value to select an `assayNames`
`assay_name`	a single `character` value for specifying which assay to use for calculation. (Please use `assay.type` instead. At some point `assay_name` will be disabled.)
`add.row`	`NULL`, `TRUE` or a `character` vector to select information from the `rowData` to add to the molten assay data. If `add.row = NULL` no data will be added, if `add.row = TRUE` all data will be added and if `add.row` is a `character` vector, it will be used to subset to given column names in `rowData`. (default: `add.row = NULL`)
`add_row_data`	Deprecated. Use `add.row` instead.
`add.col`	`NULL`, `TRUE` or a `character` vector to select information from the `colData` to add to the molten assay data. If `add.col = NULL` no data will be added, if `add.col = TRUE` all data will be added and if `add.col` is a `character` vector, it will be used to subset to given column names in `colData`. (default: `add.col = NULL`)
`add_col_data`	Deprecated. Use `add.col` instead.
`row.name`	a `character` scalar to use as the output's name for the feature identifier. (default: `row.name = "FeatureID"`)
`feature_name`	Deprecated. Use `row.name` instead.
`col.name`	a `character` scalar to use as the output's name for the sample identifier. (default: `col.name = "SampleID"`)
`sample_name`	Deprecated. Use `col.name` instead.
`...`	optional arguments: check_names: A boolean value passed to data.frame function's check.name argument. Determines if sample names are checked that they are syntactically valid variable names and are not duplicated. If they are not, sample names are modified. (default: `check_names = TRUE`)

Details

If the colData contains a column “SampleID” or the rowData contains a column “FeatureID”, they will be renamed to “SampleID_col” and “FeatureID_row”, if row names or column names are set.

Value

A tibble with the molten data. The assay values are given in a column named like the selected assay assay.type. In addition, a column “FeatureID” will contain the rownames, if set, and analogously a column “SampleID” with the colnames, if set

Author(s)

Sudarshan A. Shetty

Examples

data(GlobalPatterns)
molten_tse <- meltSE(GlobalPatterns,
                        assay.type = "counts",
                        add.row = TRUE,
                        add.col = TRUE
                        )
molten_tse

FelixErnst/mia documentation built on June 19, 2024, 3:51 a.m.