robot_2states_indexes: Returns a robot plot for selected peptides for 2 protein...

In mkajano/HDXBoxeR: Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

Returns a robot plot for selected peptides for 2 protein states.

Description

Modification of butterfly plot. x axis residues. y axis % deuteration for one variant above the axis and for second peptide below the axis. Peptides are compared between the sets for the significance change between sets. If there is significant change beteween sets peptides are plotted for all timepoints. Significanty different timepoints for the peptides are colored. Peptides ranges are plotted as a line at corresponding % deuteration values.

Usage

robot_2states_indexes(
  thP,
  th,
  indexes,
  states,
  replicates = 3,
  pvalue = 0.01,
  ylim,
  xlim,
  CI_factor = 1
)

Arguments

thP	output of output_tcourse_proc() function. Raw data for procent deuteration for time courses
th	output of output_tcourse() function. Raw data for uptake deuteration for time courses
indexes	indexes of peptides to be drawn.
states	Need to choose only two protein states
replicates	number of replicates in sample. Default set to 3.
pvalue	p-value cutoff here set up to 0.01
ylim	y-axis range
xlim	x-axis range. Set as default from max and minimum residues for the protein
CI_factor	Multiplication factor for Critical Interval. Allows for more restrictive selection of Critial interval.

Value

Robot maps for timecourses for 2 protein states and selected indexes.

Examples

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
tm_df<-output_tc(filepath=file_nm)
tmP_df<-output_tc(filepath=file_nm, percent=TRUE)
names_states<- nm_states(file_nm) ### returns states names
ind1<-robot_indexes(thP = tmP_df, th=tm_df, pvalue=0.001, CI_factor=3, states=names_states[1:2])
robot_2states_indexes(thP = tmP_df, th=tm_df,
 states=names_states[1:2],indexes =ind1, pvalue=0.001, CI_factor=3)

mkajano/HDXBoxeR documentation built on April 23, 2024, 12:28 a.m.