meltAssay {mia}R Documentation

Converting a SummarizedExperiment object into a long data.frame

Description

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

Usage

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

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

Arguments

x

A numeric matrix or a SummarizedExperiment

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)

assay_name

a character value to select an assayNames

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 currently not used.

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_name. 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,
                       add_row_data = TRUE,
                       add_col_data = TRUE,
                       assay_name = "counts")
molten_se

[Package mia version 1.0.8 Index]