meltSE: Converting a 'SummarizedExperiment' object into a long...

In microbiome/mia: Microbiome analysis

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	TreeSummarizedExperiment.
assay.type	Character scalar. Specifies which assay to use for calculation. (Default: "counts")
assay_name	Deprecated. Use assay.type instead.
add.row	Logical scalar or 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: NULL)
add_row_data	Deprecated. Use add.row instead.
add.col	Logical scalar. NULL ,or character vector. Used 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: NULL)
add_col_data	Deprecated. Use add.col instead.
row.name	Character scalar. To use as the output's name for the feature identifier. (Default: "FeatureID")
feature_name	Deprecated. Use row.name instead.
col.name	Character scalar. To use as the output's name for the sample identifier. (Default: "SampleID")
sample_name	Deprecated. Use col.name instead.
...	optional arguments: check_names: Logical scalar. 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: 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

microbiome/mia documentation built on Aug. 14, 2024, 4:42 p.m.