output_tp {HDXBoxeR}

Prepares output for HDX-MS for the deuteration uptake or percent deuteration for the time points.

Description

Returns a data frame organized for additional analysis. In columns are deuteration uptake or percent deuteration data for the given protein states. Function allows for writing csv with data, matching sequences of peptide. Protein.States, Deut.times, or number of replicates can be specified.

Usage

output_tp(
  filepath,
  replicates,
  states,
  times,
  seq_match = FALSE,
  csv = "NA",
  percent = FALSE
)

Arguments

filepath

filepath to the input file. Input file is All_results table from HDX_Examiner, where all the fields are marked for export.

replicates

number of replicates to be used in analysis. The function takes number of replicates up to specified number. If no argument provided number maximal common number of replicates it used.

states

function allows to choose what states should be used for analysis. Default all states are used.

times

lists the deuteration times to be used in analysis. Default all states used.

seq_match

Flag allows to choose if the peptide sequences should be matched between states. seq_match=FALSE signifies no sequence matching, seq_match=T states that the sequences are matched between the sets.

csv

Flag allowing saving the output as csv. With default csv="NA", data is not saved. If csv output is desided, provide output name.

percent

Flag allowing to choose output as deteuration uptake (FALSE) or percent deuteration (TRUE). Default deuteration uptake.

Value

data frame with reorganized data where in columns is the deuteration uptake for Protein States.

Examples

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
a<- output_tp(filepath=file_nm) ###all default parameters used


# all possible flags listed & percent deuteration output,
# with sequences matching for protein states.

a<-output_tp(filepath=file_nm, replicates=3, states=c("bound", "Unbound"),
times=c("3.00s", "72000.00s"), seq_match=TRUE, csv="NA", percent=TRUE)