AggregateCellMetadata: AggregateCellMetadata - take cell level metadata and collapse...

In MattPM/scglmmr: Sample-level Single-cell Generalized Linear Multilevel Models in R

AggregateCellMetadata - take cell level metadata and collapse down to sample-level metadata for use in pseudobuk testing. This can be useful if you do not already have metadata for each sample in the experiment, but these data are stored in single cell metadata. For example, metadata for the donor ID, unique sample (e.g. donorid_timepoint), age, sex etc. Note these are all individual sample level data. Single cell intrinsic variables like nUMI cannot be collapsed down, only variables that are unique for each sample which are the columns of the pseudobulk data. Only include metadata that you intend to adjust models for as covariates or random effects because all variables will be referenced during count normalization and feature filtering.

Description

AggregateCellMetadata - take cell level metadata and collapse down to sample-level metadata for use in pseudobuk testing. This can be useful if you do not already have metadata for each sample in the experiment, but these data are stored in single cell metadata. For example, metadata for the donor ID, unique sample (e.g. donorid_timepoint), age, sex etc. Note these are all individual sample level data. Single cell intrinsic variables like nUMI cannot be collapsed down, only variables that are unique for each sample which are the columns of the pseudobulk data. Only include metadata that you intend to adjust models for as covariates or random effects because all variables will be referenced during count normalization and feature filtering.

Usage

AggregateCellMetadata(
  cell.metadata,
  sample_column,
  variable_columns,
  pseudobulk.List
)

Arguments

cell.metadata	dataframe of meta data for cells-rows as columns i.e. ColData or [e-mail].
sample_column	quoted character e.g. "sample". This should indicate the variable corresponding to the rows of the pseudobulk gene expression data.
variable_columns	experiment variables coresponding to sample level data. For example: c('SubjectID', 'timepoint', 'sex', 'age').
pseudobulklist	the object output from PseudobulkList. used to check the columns of the aggregated metadata match the columns of the elements of the Pseudobulk list.

Value

Aggregated metadata

Examples

## Not run: 
samplemd = AggregateCellMetadata(cell.metadata = [e-mail], sample_column = 'sample', variable_columns = c('subjectID', 'timepoint', 'age', 'sex'), pseudobulk.List = pb)

## End(Not run)

MattPM/scglmmr documentation built on April 26, 2024, 12:55 a.m.