pcr_ttest {pcr}

t-test qPCR data

Description

t-test qPCR data

Usage

pcr_ttest(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 t.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_ttest(ct4,
          group_var = group,
          reference_gene = 'ref',
          reference_group = 'control')

# test using t.test method
pcr_test(ct4,
         group_var = group,
         reference_gene = 'ref',
         reference_group = 'control',
         test = 't.test')