meltAssay {mia}

R Documentation

Converting a SummarizedExperiment object into a long data.frame

Description

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

Usage

meltAssay(
  x,
  abund_values = "counts",
  add_row_data = NULL,
  add_col_data = NULL,
  feature_name = "FeatureID",
  sample_name = "SampleID",
  ...
)

## S4 method for signature 'SummarizedExperiment'
meltAssay(
  x,
  abund_values = "counts",
  add_row_data = NULL,
  add_col_data = NULL,
  feature_name = "FeatureID",
  sample_name = "SampleID",
  ...
)

Arguments

x	A numeric matrix or a SummarizedExperiment
abund_values	a character value to select an assayNames
add_row_data	NULL, TRUE or a character vector to select information from the rowData to add to the molten assay data. If add_row_data = NULL no data will be added, if add_row_data = TRUE all data will be added and if add_row_data is a character vector, it will be used to subset to given column names in rowData. (default: add_row_data = NULL)
add_col_data	NULL, TRUE or a character vector to select information from the colData to add to the molten assay data. If add_col_data = NULL no data will be added, if add_col_data = TRUE all data will be added and if add_col_data is a character vector, it will be used to subset to given column names in colData. (default: add_col_data = NULL)
feature_name	a character scalar to use as the output's name for the feature identifier. (default: feature_name = "FeatureID")
sample_name	a character scalar to use as the output's name for the sample identifier. (default: sample_name = "SampleID")
...	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 abund_values. 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_se <- meltAssay(GlobalPatterns,
                       abund_values = "counts",
                       add_row_data = TRUE,
                       add_col_data = TRUE
                       )
molten_se

---