Package `RBMRB`

Package ‘RBMRB’

September 22, 2017

Type Package

Title BMRB Data Access and Visualization

Version 2.1.0

Date 2017-09-22

Author Kumaran Baskaran

Maintainer Kumaran Baskaran

<[email protected]>

Description The Biological Magnetic Resonance Data Bank (BMRB,<http:// www.bmrb.wisc.edu/>) collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR(Nuclear Magnetic Resonance) spectroscopic investigations of biological macromolecules and metabolites. This package provides an interface to BMRB database for easy data access and includes a minimal set of data visualization functions. Users are encouraged to make their own data visualizations using BMRB data.

Depends R(>= 3.4.0),

License GPL-2

URL https://github.com/uwbmrb/RBMRB

, https://github.com/kumar-physics/RBMRB

LazyData TRUE

RoxygenNote 6.0.1

Imports data.table(>= 1.9.8), httr(>= 1.2.1), rjson(>= 0.2.15), ggplot2(>= 2.2.0), plotly(>= 4.5.6), stats

NeedsCompilation no

Repository CRAN

Date/Publication 2017-09-22 16:43:32 UTC

R topics documented:

atom_chem_shift_corr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2

chemical_shift_hist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

3

1

2 atom_chem_shift_corr

Index chemical_shift_hists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

4

chemical_shift_hist_res . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

5

chem_shift_corr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

6

convert_cs_to_c13hsqc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

7

convert_cs_to_n15hsqc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

7

convert_cs_to_tocsy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

8

export_star_data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

9

fetch_atom_chemical_shifts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

9

fetch_entry_chemical_shifts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

10

fetch_entry_cs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

11

fetch_res_chemical_shifts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

12

filter_residue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

12

HSQC_13C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

13

HSQC_15N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

14

makeRandomString . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

15

TOCSY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

15

16

atom_chem_shift_corr

Chemical shift correlation between given pair of atoms in a given amino acid (or) nucleic acid

Description

Plots the correlated chemical shift distribution of given pair of atoms in a single residue from BMRB database. By default it will generate interactive graphics using plotly library

Usage atom_chem_shift_corr(atom1, atom2, res = NA)

Arguments atom1 atom2 res atom name in NMR-STAR nomenclature like CA,CB2 atom name in NMR-STAR nomenclature like HA,HB2 residue name in NMR-STAR nomenclature like ALA

Value plot object

See Also

fetch_res_chemical_shifts

and

chem_shift_corr

chemical_shift_hist

Examples

#plt<-atom_chem_shift_corr('HE21','HE22','GLN')

#plots the chemical shift distribution between HE21 and HE22

3 chemical_shift_hist

Plots chemical shift distribution

Description

Plots the histogram (or) density of chemical shift distribution of a given atom from amino acid (or) nucleic acid from BMRB database. Optionally particular atom can be specified in the parameter

Usage chemical_shift_hist(res = "*", atm = "*", type = "count", bw = 0.1, cutoff = 8)

Arguments res atm type bw cutoff residue name in NMR-STAR atom nomenclature ; Example: ALA,GLY ; default

’*’ (includes everything) atom name in NMR-STAR nomenclautre ; Example :CA,HB2 default ’*’ (includes all atoms) count ; other than count will assume density plot binwith for histogram; default value 0.1ppm

values not with in the cutoff time standard deviation from both sides ofthe mean will be excluded from the plot;default value 8

Value

R plot object

See Also

fetch_res_chemical_shifts

, filter_residue

and

chem_shift_corr

and

atom_chem_shift_corr

Examples

#plt<-chemical_shift_hist('ALA')

#plots the histogram of all atoms of ALA

#plt<-chemical_shift_hist("*","CB*")

#plots CB chemical shift distribution of standard amino acids

#plt<-chemical_shift_hist('GLY',type='density')

#plots the density plot

4 chemical_shift_hists chemical_shift_hists

Plots chemical shift distribution for a list of atoms

Description

Plots the histogram (or) density of chemical shift distribution of a given list of atoms. Atoms from different residues cam be specified as "residue-atom". Exammple "ALA-CA","GLN-HE21","GLN-

HE*"

Usage chemical_shift_hists(atm = NA, type = "count", bw = 0.1, cutoff = 8, interactive = TRUE)

Arguments atm type bw cutoff interactive list Example: c("ALA-CA","GLY-CA") count ; other than count will assume density plot binwith for histogram; default value 0.1ppm

values not with in the cutoff time standard deviation from both sides ofthe mean will be excluded from the plot;default value 8

TRUE/FALSE default TRUE

Value

R plot object

See Also

fetch_res_chemical_shifts

, filter_residue

and

chem_shift_corr

and

atom_chem_shift_corr

Examples

#plt<-chemical_shift_hists(c('ALA-C*'))

#plots the histogram of all atoms of ALA

#plt<-chemical_shift_hists(c("GLY-H*","ALA-HA"),type='density')

#plots the density plot

chemical_shift_hist_res 5 chemical_shift_hist_res

Plots chemical shift distribution of all atoms of a given amino acid

Description

Plots the histogram (or) density of chemical shift distribution of all atoms of a given amino acid (or) nucleic acid from BMRB database.

Usage chemical_shift_hist_res(res = "*", type = "count", cutoff = 8, interactive = TRUE)

Arguments res type cutoff interactive residue name in NMR-STAR atom nomenclature ; Example: ALA,GLY count ; other than count will assume density plot values not with in the cutoff time standard deviation from both sides ofthe mean will be excluded from the plot;default value 8

TRUE/FALSE default TRUE

Value

R plot object

See Also

fetch_res_chemical_shifts

, filter_residue

and

chem_shift_corr

and

atom_chem_shift_corr

Examples

#plt<-chemical_shift_hist_res('ALA')

#plots the histogram of all atoms of ALA

#plt<-chemical_shift_hist('GLY',type='density')

#plots the density plot

6 chem_shift_corr chem_shift_corr

Chemical shift correlation between any two atoms from a single residue

Description

Plots the correlated chemical shift distribution of any two atoms in a single residue for the 20 standard amino acids from BMRB database. By default it will generate interactive graphics using plotly library

Usage chem_shift_corr(atom1, atom2, res = NA, type = "c", interactive = TRUE)

Arguments atom1 atom2 res type interactive atom name in NMR-STAR nomenclature like CA,CB2 atom name in NMR_STAR nomenclature like HA,HB2 residue name like ALA,GLY (optional by default includes all possible amino acids)

’c’ for contour plot and ’s’ for scatter plot default ’c’.scatter plot will be slow and heavy for large data set

TRUE/FALSE default=TRUE

Value plot object

See Also

fetch_atom_chemical_shifts

and

atom_chem_shift_corr

Examples

#plt<-chem_shift_corr('HE21','HE22')

#plots the chemical shift distribution between HE21 and HE22

convert_cs_to_c13hsqc 7 convert_cs_to_c13hsqc Reformats chemical shift dataframe for easy plotting

Description

Reformats the output dataframe from

fetch_entry_chemical_shifts

into a simple dataframe that contains proton and carbon chemical shifts in two columns. This will be helpful to plot 1H-13C

HSQC(Hetronuclear Single Quantum Coherence) spectrum

Usage convert_cs_to_c13hsqc(csdf)

Arguments csdf chemical shift data frame from

fetch_entry_chemical_shifts

Value

R data frame that contains proton and carbon chemical shifts in two columns for each residue

See Also

convert_cs_to_n15hsqc

and

convert_cs_to_tocsy

Examples df<-fetch_entry_chemical_shifts(15060)

# Downloads data from BMRB hsqc<-convert_cs_to_c13hsqc(df)

# Reformats for easy plotting convert_cs_to_n15hsqc Reformats chemical shift dataframe for easy plotting

Description

Reformats the output dataframe from

fetch_entry_chemical_shifts

into a simple dataframe that contains algorithmically combined proton and nitrogen chemical shifts in two columns. This will be helpful to plot 1H-15N HSQC(Hetronuclear Single Quantum Coherence) spectrum.

Usage convert_cs_to_n15hsqc(csdf)

8 convert_cs_to_tocsy

Arguments csdf

Chemical shift data frame from

fetch_entry_chemical_shifts

Value

R data frame that contains proton and nitrogen chemical shifts in two columns for each residue

See Also

convert_cs_to_c13hsqc

and

convert_cs_to_tocsy

Examples df<-fetch_entry_chemical_shifts(15060)

#Downloads the chemical shift data from BMRB hsqc<-convert_cs_to_n15hsqc(df)

#Reformats for easy plotting convert_cs_to_tocsy

Reformats chemical shift dataframe for easy plotting

Description

Reformats the output dataframe from

fetch_entry_chemical_shifts

into a simple dataframe that contains algorithmically combined proton shifts in two columns. This will be helpful to plot

TOCSY(TOtal Correlation SpectroscpY) spectrum

Usage convert_cs_to_tocsy(csdf)

Arguments csdf chemical shift data frame from

fetch_entry_chemical_shifts

Value

R data frame that contains all possible combinations of proton chemical shifts in two columns

See Also

convert_cs_to_c13hsqc

and

convert_cs_to_n15hsqc

Examples df<-fetch_entry_chemical_shifts(15060)

# Downloads data from BMRB tocsy<-convert_cs_to_tocsy(df)

# Reformats for easy plotting

export_star_data 9 export_star_data

Exports NMR-STAR file to BMRB API server

Description

Exports NMR-STAR file to BMRB API server for data visualization. This function will return a tocken, which can be used like a pseudo BMRB ID. The tocken will expire after 7 days

Usage export_star_data(filename)

Arguments filename filename with correct path

Value

Temporary tocken to access the file

See Also

fetch_atom_chemical_shifts

,

fetch_entry_chemical_shifts fetch_res_chemical_shifts

Examples

# ent_id <- export_star_data('/nmrdata/hpr.str')

# Exports hpr.str file to BMRB API server and gets a temporary tocken fetch_atom_chemical_shifts

Imports all chemical shifts of a given atom from BMRB database

Description

Downloads the full chemical shift data from BMRB macromolecules/metabolomics database for a given atom

Usage fetch_atom_chemical_shifts(atom = "*", db = "macromolecules")

10 fetch_entry_chemical_shifts

Arguments atom db atom name in NMR-STAR atom nomenclature ; Example: CA,CB2; default *

(all atoms) macromolecules, metabolomics (optional, by default will fetch from macromolecules database)

Value

R data frame that contains full chemical shift list for a given atom

See Also

fetch_entry_chemical_shifts

,

fetch_res_chemical_shifts

, filter_residue

and

chem_shift_corr

and

atom_chem_shift_corr

Examples

#df<-fetch_atom_chemical_shifts('CG2','macromolecules')

# Downloads CB2 chemical shifts from macromolecules database at BMRB

#df<-fetch_atom_chemical_shifts('C1','metabolomics')

# Downloads C1 chemical shifts from metabolomics database at BMRB fetch_entry_chemical_shifts

Imports chemical shift table for a given entry or list of entries from

BMRB data base

Description

Downloads NMR chemical shift data from BMRB database for a given Entry ID or list of Entry IDs

Usage fetch_entry_chemical_shifts(IDlist)

Arguments

IDlist sinlge BMRB ID (or) list of BMRB IDs in csv format; For macromolecule entries it is just a number without bmrb prefix (example: c(15060,15000,18867));

For metabolomics entries it should have ’bmse’ prefix (example: c(’bmse000035’,’bmse000035’,’bmse000036’))

Value

R data frame that contains Atom_chem_shift data for a given list of entries

See Also

fetch_atom_chemical_shifts

,

fetch_entry_cs

and

fetch_res_chemical_shifts

fetch_entry_cs

Examples df<-fetch_entry_chemical_shifts(15060)

# Downloads NMR chemical shifts of a single entry from BMRB df<-fetch_entry_chemical_shifts(c(17074,17076,17077))

# Downloads NMR chemical shifts of multiple entries from BMRB df<-fetch_entry_chemical_shifts(c('bmse000034','bmse000035','bmse000036'))

# Downloads data from BMRB metabolomics database

11 fetch_entry_cs

Imports checmial shift table for a given entry id from BMRB data base

Description

Downloads NMR chemical shift data from BMRB database for a given Entry ID

Usage fetch_entry_cs(ID)

Arguments

ID sinlge BMRB ID; For macromolecule entries it is just a number without bmrb prefix (example: 15060); For metabolomics entries it should have ’bmse’ prefix

(example: ’bmse000035’)

Value

R data frame that contains Atom_chem_shift data for a given entry ID

See Also

fetch_entry_chemical_shifts

,

fetch_atom_chemical_shifts

and

fetch_res_chemical_shifts

Examples df<-fetch_entry_cs(15060)

# Downloads NMR chemical shifts of the given entry from macromolecule database df<-fetch_entry_cs('bmse000034')

# Downloads data from BMRB metabolomics database

12 filter_residue fetch_res_chemical_shifts

Imports chemical shift data for a given amino acid/nucleic acid

Description

Downloads chemical shift data from BMRB macromolecular database for a given amino acid (or) nucleic acid. Optionally particular atom can be specified in the parameter

Usage fetch_res_chemical_shifts(res = "*", atm = "*")

Arguments res atm residue name in NMR-STAR atom nomenclature ; Example: ALA,GLY ; default

’*’ (all residues) atom name in NMR-STAR nomenclautre ; Example :CA,HB2; default * (all atoms)

Value

R data frame that contains full chemical shift list for a given atom

See Also

fetch_atom_chemical_shifts

,

filter_residue

and

chemical_shift_hist

Examples

#df<-fetch_res_chemical_shifts('GLY')

# Downloads chemical shift data of all atoms of GLY

#df<-fetch_res_chemical_shifts('ALA','CA')

# Downloads C alpha chemical shifts of ALA from macromolecules database at BMRB filter_residue

Filter for standard 20 amino acids

Description

Filters out non standard amino acids using Comp_ID. The data frame should contain three letter anio acid code in COMP_ID column.

Usage filter_residue(df)

HSQC_13C

Arguments df data frame with amino acid information in Comp_ID column

Value

R data frame that contains information from only standard 20 amino acids.

See Also

fetch_atom_chemical_shifts

Examples

#df<-filter_residue(fetch_atom_chemical_shifts("CG2"))

#Downloads all CG2 chemical shifts and removes non standard amino acids

13

HSQC_13C

Simulates H1-C13 HSQC spectra for a given entry or list of entries from BMRB

Description

Simulates H1-C13 HSQC(Hetronuclear Single Quantum Coherence) spectra directly from BMRB database. By default it will generate interactive graphics using plotly library

Usage

HSQC_13C(idlist, type = "scatter", interactive = TRUE)

Arguments idlist type interactive list of bmrb ids in csv scatter/line default=scatter

TRUE/FALSE default=TRUE

Value

R plot object

See Also

HSQC_15N

and

TOCSY

14

Examples plot_hsqc<-HSQC_13C(c(17074,17076,17077))

#Simulates C13-HSQC spectra form the given list of entries plot_hsqc<-HSQC_13C(c(17074,17076,17077),'line')

#Simulates C13-HSQC and connects the peaks with same sequence number plot_hsqc<-HSQC_13C(c(17074,17076,17077),interactive=FALSE)

#Example for non interactive plot

HSQC_15N

HSQC_15N

Simulates H1-N15 HSQC spectra for a given entry or list of entries from BMRB

Description

Simulates H1-N15 HSQC(Hetronuclear Single Quantum Coherence) spectra directly from BMRB database. Default plot type will be ’scatter’.Peaks from different spectra(entries) can be connected based on residue numbers by specifying plot type as ’line’. By default it will generate interactive graphics using plotly library

Usage

HSQC_15N(idlist, type = "scatter", interactive = TRUE)

Arguments idlist type interactive list of bmrb ids in csv scatter/line default=scatter

TRUE/FALSE default=TRUE

Value

R plot object

See Also

HSQC_13C

and

TOCSY

Examples plot_hsqc<-HSQC_15N(c(17074,17076,17077))

#simulates N15-HSQC spectra for the given 3 entreis plot_hsqc<-HSQC_15N(18857,'line')

#simulates the N15-HSQC spectra from many chemical shift lists from a single entry plot_hsqc<-HSQC_15N(c(17074,17076,17077),interactive=FALSE)

#example for non interactive plots

makeRandomString 15 makeRandomString

Generates random string of fixed length(for internal use in RBMRB)

Description

Local files may not have Entry_ID, in that case random Entry_ID is assigned using this function. It is an internal function used only by RBMRB package

Usage makeRandomString()

TOCSY

Simulates TOCSY spectra for a given entry or a list of entries from

BMRB

Description

Simulates TOCSY(TOtal Correlation SpectroscopY) spectra directly from BMRB database. By default it will generate interactive graphics using plotly library

Usage

TOCSY(idlist, interactive = TRUE)

Arguments idlist interactive list of bmrb ids c(17074,17076,17077)

TRUE/FALSE default=TRUE

Value plot object

See Also

HSQC_15N

and

HSQC_13C

Examples plot_tocsy<-TOCSY(c(17074,17076,17077))

#Simulates TOCSY spectra for the given 3 entries plot_tocsy<-TOCSY(c(17074,17076,17077),interactive=FALSE)

# Example to disable interactive plot feature

Index

atom_chem_shift_corr,

2 ,

3 –

6 ,

10

chem_shift_corr,

2 –

5 ,

6 ,

10

chemical_shift_hist,

3 ,

12

chemical_shift_hist_res,

5

chemical_shift_hists,

4

convert_cs_to_c13hsqc,

7 ,

8

convert_cs_to_n15hsqc,

7

, 7 ,

8

convert_cs_to_tocsy,

7 ,

8

, 8

export_star_data,

9

fetch_atom_chemical_shifts,

6 ,

9 , 9 ,

10 –

13

fetch_entry_chemical_shifts,

7 –

10 , 10 ,

11

fetch_entry_cs,

10 ,

11

fetch_res_chemical_shifts,

2 –

5 ,

9 –

11 ,

12

filter_residue,

3 –

5 ,

10 ,

12 , 12

HSQC_13C,

13 ,

14 ,

15

HSQC_15N,

13 ,

14 ,

15

makeRandomString,

15

TOCSY,

13 ,

14 ,

15

16

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