delta_Ct {RQdeltaCT}

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("Gene2","Gene5","Gene6","Gene9","Gene11"),
                      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 = "Gene8")
head(data.dCt)
data.dCt.exp <- delta_Ct(data.CtF.ready, ref = "Gene8", transform = TRUE)
head(data.dCt.exp)