find_ref_gene {RQdeltaCT}

find_ref_gene

Description

This function assess gene expression stability by calculation the following parameters: minimum, maximum, standard deviation, variance, and stability measures from NormFinder and geNorm algorithms. It also presents C values graphically on a line plot. This function is helpful to select the best reference gene for normalization of Ct values.

Usage

find_ref_gene(
  data,
  groups,
  candidates,
  colors,
  norm.finder.score = TRUE,
  genorm.score = TRUE,
  line.width = 1,
  angle = 0,
  x.axis.title = "",
  y.axis.title = "Ct",
  axis.title.size = 11,
  axis.text.size = 10,
  legend.title = "",
  legend.title.size = 11,
  legend.text.size = 11,
  legend.position = "top",
  plot.title = "",
  plot.title.size = 14,
  save.to.tiff = FALSE,
  dpi = 600,
  width = 15,
  height = 15,
  name.tiff = "Ct_reference_gene_selection"
)

Arguments

data

Object returned from make_Ct_ready() functions.

groups

Character vector with names of groups used for analysis. If all groups should be included to the analysis, groups parameter should be set to "all".

candidates

Character: vector of names of genes - candidates for gene reference.

colors

Character: vector of colors for genes, the number of colors should be equal to the number of candidate genes.

norm.finder.score

Logical: if TRUE, NormFinder stability score will be calculated. Default to TRUE.

genorm.score

Logical: if TRUE, geNorm stability score will be calculated. Default to TRUE.

line.width

Numeric: width of lines drawn in the plot. Default to 1.

angle

Integer: value of angle in which names of genes are displayed. Default to 0.

x.axis.title

Character: title of x axis. Default to "".

y.axis.title

Character: title of y axis. Default to "Ct".

axis.title.size

Integer: font size of axis titles. Default to 11.

axis.text.size

Integer: font size of axis text. Default to 10.

legend.title

Character: title of legend. Default to "".

legend.title.size

Integer: font size of legend title. Default to 11.

legend.text.size

Integer: font size of legend text. Default to 11.

legend.position

Position of the legend, can be "top" (default), "right", "bottom", "left", or "none" (no legend). See description for legend.position in ggplot2::theme() function.

plot.title

Character: title of plot. Default to "".

plot.title.size

Integer: font size of plot title. Default to 14.

save.to.tiff

Logical: if TRUE, plot will be saved as .tiff file. Default to FALSE.

dpi

Integer: resolution of saved .tiff file. Default to 600.

width

Numeric: width (in cm) of saved .tiff file. Default to 15.

height

Numeric: height (in cm) of saved .tiff file. Default to 15.

name.tiff

Character: name of saved .tiff file, without ".tiff" name of extension. Default to "Ct_reference_gene_selection".

Value

List containing an object with plot and a table with calculated parameters. Created plot is also displayed on the graphic device.

Examples

library(ctrlGene)
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)
ref <- find_ref_gene(data.CtF.ready,
                     groups = c("Disease","Control"),
                     candidates = c("Gene4", "Gene8","Gene10","Gene16","Gene17", "Gene18"),
                     col = c("#66c2a5", "#fc8d62","#6A6599", "#D62728", "#1F77B4", "black"),
                     norm.finder.score = TRUE,
                     genorm.score = TRUE)
ref[[2]]