calculate_normvalue: Calculate a normalized value for a subset of reference ids

In ewallace/tidyqpcr: Quantitative PCR Analysis with the Tidyverse

Calculate a normalized value for a subset of reference ids

Description

This is used to calculate the normalized 'cq' values for reference 'target_ids' (e.g. genes), to use in 'delta_cq' calculation for each 'sample_id'.

Usage

calculate_normvalue(
  value_df,
  ref_ids,
  value_name = "value",
  id_name = "id",
  norm_function = median
)

Arguments

value_df	data frame containing relevant columns, those named in 'value_name' and 'id_name' parameters.
ref_ids	values of reference ids, that are used to calculate normalized reference value.
value_name	name of column containing values. This column should be numeric.
id_name	name of column containing ids.
norm_function	Function to use to calculate the value to normalize by. Default function is median, alternatively could use mean, geometric mean, etc.

Details

Also used to calculate the normalized 'delta_cq' values for reference 'sample_ids', to use in 'deltadelta_cq' calculation for each 'target_id'.

Examples

# create simple cq dataset with one sample, two targets  and 3 reps
cq_tibble <- tibble(sample_id = "S_1",
                     target_id = rep(c("T_1",
                                       "T_norm"), each = 3),
                     tech_rep = rep(1:3, 2),
                     well_row = rep(c("A",
                                      "B"), each = 3),
                     well_col = 1,
                     well = paste0(well_row, well_col),
                     cq = c(10, 10, 10,
                            12, 12, 11))
                     
# normalise cq to reference target_id called 'T_norm'

#----- use case 1: median reference target_id value
cq_tibble |>
    calculate_normvalue(ref_ids = "T_norm",
                        value_name = "cq",
                        id_name = "target_id")

#----- use case 2: mean reference target_id value 
cq_tibble |>
    calculate_normvalue(ref_ids = "T_norm",
                        value_name = "cq",
                        id_name = "target_id",
                        norm_function = mean)

ewallace/tidyqpcr documentation built on June 5, 2024, 10:04 a.m.