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

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

Value

Examples

if (FALSE) {
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)

}