getReferenceProfileRNA: getReferenceProfileRNA

In UMMS-Biocore/dprofiler: Dprofiler:

getReferenceProfileRNA

Description

Prepares Seurat objects for Compositional Profiling

Usage

getReferenceProfileRNA(
  data,
  meta.data,
  name,
  sample_id = NULL,
  batch = NULL,
  secondary_batch = NULL,
  subset_profiledata = NULL,
  DEfield = NULL,
  DEparams = c("DESeq2", "parametric", FALSE, "Wald", "None", "Silhouette", "auto",
    "Log2FC+Padj", 1, 0.05, ""),
  max_count = 10
)

Arguments

data	profiling data
meta.data	profiling metadata
name	name of the Bulk Reference
sample_id	the field in the metadata that identifies a sample/biosample, if null, the first field will be the sample_id
batch	the batch term from the meta.data
secondary_batch	specify is there exists a secondary batch within the primary batch, e.g. Patient, or Donor
subset_profiledata	a list of subsets based on meta.data fields, the names of each element should correspond to a field in the meta.data
DEfield	the meta.data field to indicate a comparison, this should be a list with one element that this element should be a vector of two characters indicating the conditions
DEparams	DE Analysis and Computational Profiling parameters
max_count	remove genes whose maximum count is below a small count (e.g. 10)

UMMS-Biocore/dprofiler documentation built on Oct. 16, 2022, 11:37 a.m.