calculate_efficiency: Calibrate primer sets / probes by calculating detection...

In ewallace/tidyqpcr: Quantitative PCR Analysis with the Tidyverse

Calibrate primer sets / probes by calculating detection efficiency and R squared

Description

Note efficiency is given in ratio, not per cent; multiply by 100 for that.

Usage

calculate_efficiency(cq_df_1, formula = cq ~ log2(dilution) + biol_rep)

Arguments

cq_df_1	data frame with cq (quantification cycle) data, 1 row per well. Must have columns cq, dilution. Assumes data are only for 1 probe/primer set/target_id, i.e. all values in cq_df_1 are fit with the same slope.
formula	formula to use for log-log regression fit. Default value assumes multiple biological replicates, cq ~ log2(dilution) + biol_rep. If only a single Biological Replicate, change to cq ~ log2(dilution).

Value

data frame with 1 single row, and columns: efficiency, efficiency.sd, r.squared.

See Also

calculate_efficiency_bytargetid

Examples

# create simple dilution dataset
dilution_tibble <- tibble(dilution = rep(c(1, 0.1, 0.001, 0.0001), 2),
                     cq = c(1, 3, 4, 6,
                            4, 5, 6, 7),
                     biol_rep = rep(c(1,2), each = 4),
                     target_id = "T1")
                     
# calculate primer efficiency

#----- use case 1: include difference across replicates in model
dilution_tibble |>
    calculate_efficiency()

#----- use case 2: ignore difference across replicates
dilution_tibble |>
    calculate_efficiency(formula = cq ~ log2(dilution))

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