add_stat_dependency: Calculates confidence limits

In michbur/HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Calculates confidence limits

Description

Returns relation with confidence limits for each peptide.

Usage

add_stat_dependency(
  calc_dat,
  confidence_limit = 0.98,
  theoretical = FALSE,
  relative = TRUE
)

Arguments

calc_dat	processed data from DynamX file - using prepare_dataset
confidence_limit	confidence limit chosen by user - from range [0, 1].
theoretical	logical value to determine if the plot is theoretical or not.
relative	logical value to determine if values are relative or absolute.

Details

...

Value

calc_dat extended by column specifying if given peptide is relevant in given confidence limit. The value of the confidence limit is added as an attribute - as well as parameters used to calculate (theoretical/relative)

See Also

read_hdx prepare_dataset

Examples

#load example data
dat <- read_hdx(system.file(package = "HaDeX", 
                            "HaDeX/data/KD_180110_CD160_HVEM.csv"))
                            
# prepate dataset for states `CD160` and `CD160_HVEM` in given time parameters 
calc_dat <- prepare_dataset(dat,
                            in_state_first = "CD160_0.001",
                            chosen_state_first = "CD160_1",
                            out_state_first = "CD160_1440",
                            in_state_second = "CD160_HVEM_0.001",
                            chosen_state_second = "CD160_HVEM_1",
                            out_state_second = "CD160_HVEM_1440") 
                            
# add calculated confidence limits for prepared data
add_stat_dependency(calc_dat, 
                    confidence_limit = 0.98, 
                    theoretical = FALSE, 
                    relative = TRUE)
                     

michbur/HaDeX documentation built on March 29, 2022, 5:46 p.m.