get_diff: Differential expression analysis

In AllenSpike/CPDR: Cancer Drug Personalized Recommendation (CDPR)

Differential expression analysis

Description

Differential expression analysis

Usage

get_diff(
  data = NULL,
  DE_method = "edgeR",
  normalize_samples = TRUE,
  threshold_log2foldchange = 2.5,
  threshold_pval = 0.05,
  threshold_adjpval = 0.001,
  k = 1,
  n_topGenes = 500,
  parallel_cores = 2
)

Arguments

data	The purified profiles of subgoups and control groups for each clinical query sample
DE_method	edgeR, DESeq2 or limma DE analysis.
normalize_samples	if TRUE, RUVSeq normalization is applied to either EdgeR or DESeq. No normalization needed for limma+voom.
threshold_log2foldchange	threshold for log2foldchange. 2.5 by default.
threshold_pval	threshold for pvalue. 0.05 by default.
threshold_adjpval	threshold for adjusted pvalue. 0.001 by default.
k	either k=1 (by default), k=2 or k=3, number of factors used in model matrix construction in RUVSeq normalization if normalize_samples=TRUE.
n_topGenes	number of empiricaly differentially expressed genes estimated for RUVSeq normalization. Default is 5000.
parallel_cores	number of cores to be used for parallel computing in DESeq2.

Value

A list with list of differentially expressed genes.

AllenSpike/CPDR documentation built on April 18, 2022, 4:38 p.m.