quality_control: Experiment quality control

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

Description

Checks how the uncertainty changes in a function of 'out_time'.

Usage

quality_control(dat, state_first, state_second, chosen_time, in_time)

Arguments

dat	data read by read_hdx
state_first	state of the first peptide
state_second	state of the second peptide
chosen_time	chosen time point
in_time	'in' time

Details

The function calculates mean uncertainty of all peptides and its uncertainty (standard error) based on given 'in_time' and 'chosen_time' as a function of 'out_time'. Both theoretical and experimental results for each state and their difference are supplied for comparison but only experimental calculations depends on 'out_time' variable. The results are either in form of relative or absolute values depending on the 'relative' parameter supplied by the user. This data can be useful for general overview of the experiment and analyse of the chosen time parameters.

Value

data.frame with mean uncertainty per different 'out_time' value

See Also

read_hdx

Examples

# load example data
dat <- read_hdx(system.file(package = "HaDeX", "HaDeX/data/KD_180110_CD160_HVEM.csv"))

# calculate mean uncertainty 
(result <- quality_control(dat = dat,
                           state_first = "CD160",
                           state_second = "CD160_HVEM", 
                           chosen_time = 1, 
                           in_time = 0.001))    
                           
# load extra libraries
library(ggplot2)
library(tidyr)
library(dplyr)

# example of data visualization 
gather(result, 2:7, key = 'type', value = 'value') %>%
filter(startsWith(type, "avg")) %>%
  ggplot(aes(x = factor(out_time), y = value, group = type)) +
  geom_line(aes(color = type)) +
  labs(x = "Out time", 
       y = "Mean uncertainty")

HaDeX documentation built on Aug. 12, 2021, 5:20 p.m.