run_cna_workflow: Run the CNA workflow

In rdocking/amlpmpsupport: Support Functions for AML PMP RNA-Seq Stratification Manuscript

Description

Run the CNA workflow

Usage

run_cna_workflow(
  expr.mat,
  genes.bed,
  window_size = NA,
  mean_tpm_threshold = 0,
  cv_threshold = 0,
  reference_labels,
  scale_samples_by_zero = TRUE
)

Arguments

expr.mat	A matrix of gene-expression values
genes.bed	A bed-like file of gene coordinates
window_size	Window size to use for rolling mean
mean_tpm_threshold	TPM threshold to retain genes
cv_threshold	CV threshold to retain genes
reference_labels	Reference labels
scale_samples_by_zero	Scale samples by zero?

Value

A re-scaled matrix

rdocking/amlpmpsupport documentation built on Jan. 4, 2021, 7:09 a.m.