HDXBoxeR (version 0.0.2)

robot_indexes: Returns indexes for peptides with significant difference between two sets

Description

Function to help decide which peptides will be drawn on Robot plots.

Usage

robot_indexes(thP, th, replicates = 3, pvalue = 0.01, states, CI_factor = 1)

Value

Returns indexes of significant peptides

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

replicates

number of replicates in sample. Default set to 3.

pvalue

p-value cutoff. Default set up to 0.01

states

Protein states from the set. As default all states are chosen.

CI_factor

Multiplication factor for Critical Interval. Allows for more restrictive selection of Critial interval.

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)

 # more restictive peptide selection
robot_indexes(thP = tmP_df, th=tm_df, pvalue=0.01, CI_factor=1.5)