delta_Ct: delta_Ct

In RQdeltaCT: Relative Quantification of Gene Expression using Delta Ct Methods

delta_Ct

Description

This function calculates delta Ct (dCt) values by subtracting Ct values of reference gene or genes from Ct values of remaining genes. Obtained dCt values can be further transformed by using 2^-dCt formula (if transform == TRUE).

Usage

delta_Ct(
  data,
  ref,
  normalise = TRUE,
  transform = FALSE,
  save.to.txt = FALSE,
  name.txt = "data_dCt"
)

Arguments

data	Data object returned from make_Ct_ready function.
ref	Character vector with name of one or more reference genes.
normalise	Logical: if TRUE, data normalisation will be done using reference gene/genes (provided in ref parameter).
transform	Logical: if TRUE, calculated dCt values will be transformed using 2^-dCt formula. Default to FALSE.
save.to.txt	Logical: if TRUE, returned data will be saved to .txt file. Default to FALSE.
name.txt	Character: name of saved .txt file, without ".txt" name of extension. Default to "data_dCt".

Value

Data frame with dCt values.

Examples

library(tidyverse)
data(data.Ct)
data.CtF <- filter_Ct(data.Ct,
                      remove.Gene = c("FGF23","ANGPT2","IL1A","CSF2","IL6"),
                      remove.Sample = c("Control08","Control16","Control22"))
data.CtF.ready <- make_Ct_ready(data.CtF, imput.by.mean.within.groups = TRUE)
data.dCt <- delta_Ct(data.CtF.ready, ref = "GAPDH")
head(data.dCt)
data.dCt.exp <- delta_Ct(data.CtF.ready, ref = "GAPDH", transform = TRUE)
head(data.dCt.exp)

RQdeltaCT documentation built on April 4, 2025, 12:53 a.m.