BulkDesignMatrix: BulkDesignMatrix - designmatrix for the main experiment...

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

BulkDesignMatrix - designmatrix for the main experiment factor - used in normalization

Description

BulkDesignMatrix - designmatrix for the main experiment factor - used in normalization

Usage

BulkDesignMatrix(metadata, sample_column, variable_column, pseudobulklist)

Arguments

metadata	dataframe of meta data for cells-rows variables-columns i.e. ColData or seuratmeta.data
sample_column	quoted character e.g. "sample" the subject level sample variable - if multiple timepoints should be subjectID_timepoint i.e. s1_0, s1_1
variable_column	the main experiment variable of interest e.g. timepoint or if implementing custom contrasts for difference in foldchange between groups, a combined factor of group_time, e.g. pooroutcome_t0, pooroutcome_t1, goodoutcome_t0, goodoutcome_t1 additional covariates can be specified in dreamMixedModel
pseudobulklist	the list created with PseudobulkList

Value

a design matrix

Examples

## Not run: 
designmat = scglmmr::BulkDesignMatrix(metadata = meta, sample_column = "sample",
variable_column = "cohort_timepoint", pseudobulklist = pb)

## End(Not run)

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