qpcr_analysis: qPCR analysis

In dcorujog/qpcr-package: Analysis of qPCR data with the delta Ct method

qPCR analysis

Description

A function for the analysis of qPCR data using the "delta Ct" method.

Usage

qpcr_analysis(
  ct_data,
  design,
  calibsample,
  hkg,
  exp_name = "Experiment",
  fix_names = FALSE,
  exclude = FALSE,
  save_csv = TRUE,
  qc_plots = TRUE,
  out_dir = getwd()
)

Arguments

ct_data	a data frame with the qPCR input data. It needs to have the following columns: names, cq, efficiency, primers, included.
design	a data frame containing the experimental design, at least one expected column called "sample_name" which has to match the sample names in ct_data and additional columns for each experimental condition relevant in the design.
calibsample	a character string with the name of the sample to be used as reference for dct calculation. This sample will have an expression value of 1 for all targets and the rest of the samples will have values expressing their relative expression to this sample.
hkg	a character vector with the name of the "housekeeping" genes used for normalization.
exp_name	a character string with the name of the experiment, which will be used to name the files and objects generated by the function
fix_names	logical indicating whether the sample names need to be "fixed" (default = FALSE, only relevant if directly using files generated with chainy to remove well position, dots and asterisks from sample names).
exclude	logical indicating whether the logical column "exclude" from the input should be used to filter the data frame (default = FALSE).
save_csv	logical indicating whether to save the final analyzed data frame as a csv file.
qc_plots	logical indicating whether to generate and save QC plots.
out_dir	directory for saving all results and plots (default = working directory)

Value

a data frame with the analyzed qPCR data containing normalized dct values.

dcorujog/qpcr-package documentation built on Sept. 4, 2023, 3:04 p.m.