RunVoomLimma_covar: RunVoomLimma_covar RunLimmaVoom with an option to adjust for...

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

RunVoomLimma_covar RunLimmaVoom with an option to adjust for a covariate within mRNA.

Description

RunVoomLimma_covar RunLimmaVoom with an option to adjust for a covariate within mRNA.

Usage

RunVoomLimma_covar(
  dgelists,
  design_matrix,
  co_variable_genes = NULL,
  grouptable,
  do_contrast_fit,
  my_contrast_matrix,
  my_model_metadata,
  celltypes.vector = NULL,
  parallel.sz = 4
)

Arguments

dgelists	DGElists created with PseudobulkList
design_matrix	design matrix created with BulkDesignMatrix
co_variable_genes	co variable genes
grouptable	argument to gsva
do_contrast_fit	do contrasts
my_contrast_matrix	contrast matrix
my_model_metadata	model metadata
celltypes.vector	vector of celltypes assign as names of dgeList

Examples

## Not run: 
RunVoomLimma_covar(dgelists = dge_lists, design_matrix = design, co_variable_genes = NULL, grouptable = grouptable ,do_contrast_fit = TRUE,
 my_contrast_matrix = c_mat, my_model_metadata = md, celltypes.vector = NULL, parallel.sz = 4)


## End(Not run)

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