eff.plot: Plot concentration curve and linear regression.

In jrijn/Rsome: Analyse RT-qPCR Data

Description

This function plots the untransformed Cq values for each target against the log2([cDNA]). Then it performs linear regression and plots the R^2 and y ~ x formula.

Usage

eff.plot(tablename, logConcentration = "logConcentration",
  groupColumn = "Target", meanCq = "meanCq", plotWidth = 10,
  plotHeight = 10)

Arguments

tablename:	a relex object with an added column of log2([cDNA]) called logConcentration
groupColumn:	defaults to "Target". Defines the grouping column which will define coloring.
logConcentration:	defaults to "logConcentration". Defines the column containing log2([cDNA]) values.
meanCq:	defaults to "meanCq". Defines the column containing meanCq values.
plotWidth:	width of output pdf file
plotHeight:	height of output pfd file

Examples

cq <- Rsome::cqimport(cqfile)
mc <- Rsome::mcimport(
  cqimport = cq, 
  meltderivative = meltfile)
  
re <- Rsome::relex(
  cq, 
  household = "Gapdh",
  SDcutoff = 1,
  Cqcutoff = 35)

library(tidyr)
library(dplyr)

eff <- separate(re, "Sample", c("Exp", "Condition", "Concentration"), sep = "_")
eff$Concentration <- as.numeric(eff$Concentration)
eff <- eff %>%
  filter(Concentration > 0) %>%
  mutate(logConcentration = log2(Concentration))

p1 <- eff.plot(
  eff,
  logConcentration = "logConcentration",
  groupColumn = "Target",
  meanCq = "meanCq")
  

jrijn/Rsome documentation built on April 13, 2020, 7:52 p.m.