plot_qpcr: Plot the qPCR results

In HaojiaWu/plot1cell: A package for single cell data visualization

Plot the qPCR results

Description

This function is to process the Cq file generated by the qPCR machine in our lab.

Usage

plot_qpcr(qPCR_file, metadata_file, ref_gene, ref_sample, file_name)

Arguments

qPCR_file	Path to the Cq file from qPCR machine. Must be in csv format.
metadata_file	Path to the metadata file to assign your samples into groups. Must be in csv format.
ref_gene	The gene used for normalization. e.g. GAPDH.
ref_sample	The sample used as reference sample. e.g. sample from the control group.
file_name	The output file name

Value

There are three output files produced from this script. The csv file contains the average quantitative value (2^-ΔΔCt) for each sample (and each gene) after normalized by the reference gene (e.g. GAPDH) and the reference sample (e.g. sample from the control group). This file can be input into Graphpad Prism. The txt file includes all statistics from comparisons of any two given groups. If the run has two groups only, Welch's t test will be performed. Otherwise, one-way ANOVA with post-hoc Tukey's test will be performed. Finally, the tiff file is a boxplot graph to visualize the gene expression across groups.

HaojiaWu/plot1cell documentation built on Nov. 13, 2023, 9:20 a.m.