seAMLess: Given the count matrices of bulk-RNA samples, this function...

In seAMLess: A Single Cell Transcriptomics Based Deconvolution Pipeline for Leukemia

Given the count matrices of bulk-RNA samples, this function deconvolutes each sample into its cell types using a healthy BM reference, and calculates the sample's in vitro resistance to Venetoclax.

Description

Given the count matrices of bulk-RNA samples, this function deconvolutes each sample into its cell types using a healthy BM reference, and calculates the sample's in vitro resistance to Venetoclax.

Usage

seAMLess(
  mat,
  scRef = seAMLessData::scRef,
  scRef.sample = "Sample",
  scRef.label = "label.new",
  verbose = TRUE
)

Arguments

mat	count matrix (genes by 1+samples).
scRef	reference matrix for single cell data
scRef.sample	column name for the samples in single cell reference
scRef.label	column name for the cell names in single cell reference
verbose	prints detailed messages

Value

List of deconvoluted cell type percentages and predicted drug resistances

seAMLess documentation built on April 3, 2025, 7:51 p.m.