buildReferencePanel: Function to build a reference panel from your bulk RNA...

In linquynus/RCAv2-beta: Reference Component Analysis

Description

Function to build a reference panel from your bulk RNA sequencing data

Usage

buildReferencePanel(
  bulk.rna.data,
  celltype.vec = colnames(bulk.rna.data),
  fc.thrs = 7.5,
  fdr.thrs = 0.01,
  gene.nomenclature = "SYMBOL",
  species = "HUMAN",
  folder.path = ".",
  filename = "my_reference_panel.rds"
)

Arguments

bulk.rna.data	Bulk RNA sequencing data - ideally TPM normalized.
celltype.vec	Vector of cell type names of each bulk RNA sequencing sample.
fc.thrs	fold change threshold
fdr.thrs	FDR threshold
gene.nomenclature	Type of gene nomenclature. "ENS" for Ensembl IDs, "SYMBOL" for gene symbols. Default is "SYMBOL".
species	"HUMAN" for human data, "MOUSE" for mouse data. Default is "HUMAN".
folder.path	path to store reference panel
filename	file name of reference panel (should end with .rds)

linquynus/RCAv2-beta documentation built on Aug. 9, 2020, 12:34 a.m.