DE.status: Differential Expression status calculator for RNA-seq data

In sebastian-gregoricchio/Rseb: An R-package for NGS data managing and visualization

Differential Expression status calculator for RNA-seq data

Description

Defines the differential expression status of genes from RNA-seq data depending on fold change expression and adjusted p-value.

Usage

DE.status(
  log2FC,
  p.value.adjusted,
  FC_threshold = 1.5,
  FC_NoResp_left = 0.9,
  FC_NoResp_rigth = NULL,
  p.value_threshold = 0.05,
  low.FC.status.label = "DOWN",
  high.FC.status.label = "UP",
  unresponsive.label = "NoResp",
  null.label = "NULL"
)

Arguments

log2FC	Numeric vector of log2(fold change expression) values.
p.value.adjusted	Numeric vector of p-values. Use of adjusted p-values is recommended.
FC_threshold	Value of the threshold to use for the fold change expression to define differentially expressed genes, expressed as linear value. By default 1.5 and by consequence 1/1.5.
FC_NoResp_left	Value of the threshold to use for the fold change expression to define unresponsive genes when FC < 1, expressed as linear value. By default 0.9. If NULL it will be calculated symmetrically from FC_NoResp_rigth as 1/FC_NoResp_rigth.
FC_NoResp_rigth	Value of the threshold to use for the fold change expression to define unresponsive genes when FC > 1, expressed as linear value. By default 1.1. If NULL it will be calculated symmetrically from FC_NoResp_left as 1/FC_NoResp_left.
p.value_threshold	Value of the threshold to use for the p-values to define differentially expressed genes, expressed as linear value. By default 0.05.
low.FC.status.label	String to define the label indicating the differentially expressed genes with a FoldChange < FC_threshold.
high.FC.status.label	String to define the label indicating the differentially expressed genes with a FoldChange > FC_threshold.
unresponsive.label	String to define the label indicating the unresponsive genes identified as FC_NoResp_left < FoldChange < FC_NoResp_rigth and p.value > p.value.threshold.
null.label	String to define the label indicating the null genes.

Value

It returns a vector containing the differential expression status for each original value in the same order used in the input.

sebastian-gregoricchio/Rseb documentation built on May 15, 2024, 5:45 a.m.