RefDB_data: RefDB object

In BaMORC: Bayesian Model Optimized Reference Correction Method for Assigned and Unassigned Protein NMR Spectra

Description

Collection of data from Re-referenced Protein Chemical shift Database (RefDB) and their access functions.

Usage

RefDB_data

Format

A class contains 1557 13C datasets and access functions.

Details

$AminoAcid

data set of 19 amino acid single-letter naming convention (excluding glycine)

$carbonDat

data set (list) of all 1557 RefDB carbon 13 raw data pre-processed in data frame format

$carbonDat_narm

data set (list) of all 1557 RefDB carbon 13 raw data pre-processed in data frame format with NA removed

$carbonDat_rmGU

data set (list) of all 1557 RefDB carbon 13 raw data pre-processed in data frame format with NA, glycine and undetermined secondary structure elements removed

$DBID

data set of all 1557 RefDB IDs

$getData(index = NA, ID = NA, type = "raw")

function that return single dataset, (index or ID, only one is allowed)

• index. the index of the dataset

• ID. the RefDB ID number of the dataset

• type what kind of data will be fetched. "raw": returns raw data; "datatable": return data in data frame format; "rmNA": return data with NA removed; "rmGU: return data with NA, glycine and undetermined secondary structure elements removed

$getFreq(index = NA, ID = NA)

function that return amino acid relative cumulative frequency for each data set (index or ID, only one is allowed)

$getSecStr(index = NA, ID = NA)

function that return secondary structure information for each data set (index or ID, only one is allowed)

$getSequence(index = NA, ID = NA)

function that return protein sequence information for each data set (index or ID, only one is allowed)

$rawData

the data set contains all the raw data from RefDB

BaMORC documentation built on May 1, 2019, 6:35 p.m.