pcr_wilcox: Wilcoxon test qPCR data

In MahShaaban/pcr: Analyzing Real-Time Quantitative PCR Data

Wilcoxon test qPCR data

Description

Wilcoxon test qPCR data

Usage

pcr_wilcox(df, group_var, reference_gene, reference_group, tidy = TRUE, ...)

Arguments

df	A data.frame of C_T values with genes in the columns and samples in rows rows
group_var	A character vector of a grouping variable. The length of this variable should equal the number of rows of df
reference_gene	A character string of the column name of a control gene
reference_group	A character string of the control group in group_var
tidy	A logical whether to return a list of htest or a tidy data.frame. Default TRUE.
...	Other arguments to wilcox.test

Value

A data.frame of 5 columns

• gene The column names of df. reference_gene is dropped

• estimate The estimate for each term

• p_value The p-value for each term

• lower The low 95% confidence interval

• upper The high 95% confidence interval

When tidy is FALSE, returns a list of htest objects.

Examples

# locate and read data
fl <- system.file('extdata', 'ct4.csv', package = 'pcr')
ct4 <- read.csv(fl)

# make group variable
group <- rep(c('control', 'treatment'), each = 12)

# test
pcr_wilcox(ct4,
           group_var = group,
           reference_gene = 'ref',
           reference_group = 'control')

# test using wilcox.test method
pcr_test(ct4,
         group_var = group,
         reference_gene = 'ref',
         reference_group = 'control',
         test = 'wilcox.test')

MahShaaban/pcr documentation built on Jan. 23, 2023, 11:37 p.m.