Package ‘aaSEA’

November 9, 2019
Type Package
Title Amino Acid Substitution Effect Analyser
Version 1.1.0
Author Raja Sekhara Reddy D.M
Maintainer Raja Sekhara Reddy D.M <raja.duvvuru@gmail.com>
Description
Given a protein multiple sequence alignment, it is daunting task to assess the effects of substitu-
tions along sequence length. 'aaSEA' package is intended to help researchers to rapidly anal-
yse property changes caused by single, multiple and correlated amino acid substitutions in pro-
teins. Methods for identification of co-evolving positions from multiple sequence align-
ment are as described in : Pelé et al., (2017) <doi:10.4172/2379-1764.1000250>.
Depends R(>= 3.4.0)
Imports DT(>= 0.4), networkD3(>= 0.4), shiny(>= 1.0.5),
shinydashboard(>= 0.7.0), magrittr(>= 1.5), Bios2cor(>= 2.0),
seqinr(>= 3.4-5), plotly(>= 4.7.1), Hmisc(>= 4.1-1)
License GPL-3
Encoding UTF-8
LazyData true
RoxygenNote 6.1.1
Suggests knitr, rmarkdown
VignetteBuilder knitr
NeedsCompilation no
Repository CRAN
Date/Publication 2019-11-09 16:20:02 UTC

R topics documented:
AAindex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
corSubFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Cruciani . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1
2 AAindex

Fasgai . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
getAASub . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
getCorPropChange . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
getCorSites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
getPropChange . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
getPropCorr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
getTopSub . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Kidera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
matEncode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
plotCorNet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
plotCorSubChanges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
plotMultiSubChange . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
plotSingleSubChange . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
startSeaShiny . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Index 13

AAindex A data frame of 533 amino acid properties from AAindex.

Description
A data frame of 533 amino acid properties.

Usage
AAindex

Format
A data frame with 533 rows and 20 variables:
name amino acid property as in AAindex
A Alanine, Ala, A
C Cysteine, Cys, C
D Aspartate, Asp, D
E Glutamate, Glu, E
F Phenylalanine, Phe, F
G Glycine, Gly, G
H Histidine, His, H
I Isoleucine, Ile, I
K Lysine, Lys, K
L Leucine, Leu, L
M Methionine, Met, M
N Asparagine, Asn, N
corSubFile 3

P Proline, Pro, P
Q Glutamine, Gln, Q
R Arginine, Arg, R
S Serine, Ser, S
T Threonine, Thr, T
V Valine, Val, V
W Tryptophan, Trp, W
Y Tyrosine, Tyr, Y ...

corSubFile A data frame of correlated sites.

Description
This file is output of ’getTopSub’ function with subset of alignment as input. This subset alignment
is output of ’getCorSite’ function

Usage
corSubFile

Format
A data frame with 2 Columns representing positional pairs:
Pos1 Position one prefixed with Wt amino acid and suffixed with substitution
Pos2 Position two prefixed with Wt amino acid and suffixed with substitution ...

Cruciani A data frame of 3 Cruciani properties for 20 amino acids.

Description
A data frame of 3 Cruciani properties for 20 amino acids.

Usage
Cruciani

Format
A data frame with 20 rows and 3 columns representing amino acids and Cruciani properties:
Names of amino acids
PP1 Polarity
PP2 Hydrophobicity
PP3 H-bonding ...
4 getAASub

Fasgai A data frame of six Fasgai vectors for 20 amino acids.

Description
A data frame of six Fasgai vectors for 20 amino acids.

Usage
Fasgai

Format
A data frame with 20 rows and 6 columns representing amino acids and Fasgai vectors:
Names of amino acids
F1 Hydrophobicity index
F2 Alpha and turn propensities
F3 Bulky properties
F4 Compositional characteristic index
F5 Local flexibility
F6 Electronic properties ...

getAASub Get amino acid substitutions from multiple sequence alignment

Description
Get amino acid substitutions from multiple sequence alignment

Usage
getAASub(fileLoc)

Arguments
fileLoc exact location of multiple sequence alignment file in "FASTA" format

Value
Returns a list of two data frames 1.Single substitutions 2.Multiple substitutions

Examples
file = system.file("extdata", "linB_Prot_ali.fasta", package = "aaSEA")
getAASub(fileLoc = file)
getCorPropChange 5

getCorPropChange Get property changes associated with correlated substitutions

Description
Get property changes associated with correlated substitutions

Usage
getCorPropChange(corSubFile, propertyDF = "Cruciani",
propertyIndex = 1)

Arguments
corSubFile A dataframe with two columns i.e. Pos1 and Pos2. This file is generated by
getTopSub
propertyDF Choose one of Cruciani, Fasgai, Kidera or AAindex based amino acid properties
propertyIndex The amino acid property to analyse. It is row number in propertyDF data frame

Value
A data frame of 12 columns consisting data regarding Wild type and mutant resides and their posi-
tions alogn with their properties and net changes between Pos1 and Pos2

Examples
getCorPropChange(corSubFile = corSubFile, propertyDF = "Cruciani", propertyIndex = 1)

getCorSites Get correlated sites with substitutions

Description
Get correlated sites with substitutions

Usage
getCorSites(fileLoc, corMethod = "mcbasc")

Arguments
fileLoc exact location of multiple sequence alignment file in "FASTA" format
corMethod One of the methods to compute correlated sites viz. ’mip’, ’elsc’, ’mcbasc’ and
’omes’. Default is ’mcbasc’.
6 getPropChange

Value

A subset alignment matrix of original multiple sequence alignment with significant correlations.

Examples
file = system.file("extdata", "linB_toy_ali.fasta", package = "aaSEA")
getCorSites(fileLoc = file,corMethod="mcbasc")

getPropChange Get wild type and substituted amino acid properties and associated
property changes

Description

Get wild type and substituted amino acid properties and associated property changes

Usage

getPropChange(subFile, propertyDF = "Cruciani", propertyIndex = 1)

Arguments

subFile A data frame of single or multiple substitutions obtained using ’getAASub’

function
propertyDF Choose one of Cruciani, Fasgai, Kidera or AAindex based amino acid properties
propertyIndex The amino acid property to analyse. It is row number in propertyDF data frame

Value

A substitution data frame with three additional columns i.e. wt.Prop, mu.Prop and Delta.Prop

Examples
ssFileLoc <- system.file("extdata", "singleSub.rda", package = "aaSEA")
singleSubFile <- readRDS(ssFileLoc)
msFileLoc <- system.file("extdata", "multiSub.rda", package = "aaSEA")
multiSubFile <- readRDS(msFileLoc)
getPropChange(subFile = singleSubFile, propertyDF = "Cruciani", propertyIndex = 1)
getPropChange(subFile = multiSubFile, propertyDF = "Cruciani", propertyIndex = 1)
getPropCorr 7

getPropCorr Get amino acid property wise correlations of co-evolving columns of

a multiple sequence alignment

Description
Get amino acid property wise correlations of co-evolving columns of a multiple sequence alignment

Usage
getPropCorr(selMat, propertyDF = "Cruciani", propertyIndex = 1)

Arguments
selMat A subset matrix of original multiple sequence alignment with significant corre-
lations identified with ’getCorSites’ function
propertyDF One of the amino acid property data frames. viz. Cruciani, Fasgai, Kidera,
AAindex. Default is Cruciani properties
propertyIndex Specific property row number from the data frame of propertyDF

Value
A data frame of four columns viz. Pos1, Pos2, Cor and p Value. Results are filtered to find position
pairs with correlations above 0.8 and below -0.8

Examples
selMatLoc <- system.file("extdata", "selMat.rda", package = "aaSEA")
selMat <- readRDS(selMatLoc)
getPropCorr(selMat = selMat, propertyDF = "Cruciani", propertyIndex = 1)

getTopSub Get sites with more than one-correlated substitutions other than con-
served amino acids at that position

Description
Get sites with more than one-correlated substitutions other than conserved amino acids at that posi-
tion

Usage
getTopSub(selMat)
8 Kidera

Arguments
selMat A subset matrix of original multiple sequence alignment with significant corre-
lations identified with ’getCorSites’ function

Value
A data frame with two columns i.e. Pos1 and Pos2 which is a filtered subset of many correlated
substitutions based on frequency of substitution after consensus of a column in multiple sequence
alignment

Examples
selMatLoc <- system.file("extdata", "selMat.rda", package = "aaSEA")
selMat <- readRDS(selMatLoc)
getTopSub(selMat = selMat)

Kidera A data frame of 10 Kidera factors for 20 amino acids

Description
A data frame of 10 Kidera factors for 20 amino acids.

Usage
Kidera

Format
A data frame with 20 rows and ten columns representing 20 amino acids and 10 kidera factors:

Names of amino acids

KF1 Helix/bend preference
KF2 Side-chain size
KF3 Extended structure preference
KF4 Hydrophobicity
KF5 Double-bend preference
KF6 Partial specific volume
KF7 Flat extended preference
KF8 Occurrence in alpha region
KF9 pK-C
KF10 Surrounding hydrophobicity ...
matEncode 9

matEncode Function to encode Correlated columns of alignment matrix with de-

sired properties

Description
Function to encode Correlated columns of alignment matrix with desired properties

Usage
matEncode(aliMat, pIndex, propDf)

Arguments
aliMat amino acid multiple sequence alignment in the form of a matrix
pIndex Amino acid property index to be encoded. It is the row number in the property
data frame
propDf The amino acid property to analyse. It is row number in propertyDF data frame

Value
A matrix of input dimensions with amino acid alphabets replaced by amino acid properties of choice

Examples
aliMatLoc <- system.file("extdata", "aliMat.rda", package = "aaSEA")
aliMat <- readRDS(aliMatLoc)
matEncode(aliMat = aliMat, pIndex = 1, propDf = "Cruciani" )

plotCorNet simple interactive network diagram of correlated substitution pairs

Description
simple interactive network diagram of correlated substitution pairs

Usage
plotCorNet(corSubDF)

Arguments
corSubDF A data frame with two columns i.e. Pos1 and Pos2. This file is generated by
’getTopSub’ function.
10 plotCorSubChanges

Value

An interactive network diagram of correlated substitution pairs.

Examples

corSub <- corSubFile

plotCorNet(corSubDF = corSub)

plotCorSubChanges Plot co-evolving sites with selected property correlations

Description

Plot co-evolving sites with selected property correlations

Usage

plotCorSubChanges(corSitePropChange)

Arguments
corSitePropChange
A data frame of coevolving sites and associated property changes obtained by
"getPropCorr" function with selected MSA matrix (selMat) and desired property
selected from property data frame and property index.

Value

Returns an interactive heat map of significant sites with selected property correlations

Examples

fileLocation <- system.file("extdata", "corSitePropChangeDF.rda", package = "aaSEA")

corSitePropChange <- readRDS(fileLocation)
plotCorSubChanges(corSitePropChange = corSitePropChange)
plotMultiSubChange 11

plotMultiSubChange Plots heat map of multiple substitution associated changes per site

Description
Plots heat map of multiple substitution associated changes per site

Usage
plotMultiSubChange(multiSubChangeDF)

Arguments
multiSubChangeDF
A data frame of multiple amino acid substitutions per site calculated with ’getAA-
Sub’ and associated property changes obtained by calling ’getPropChange’ func-
tion

Value
An interactive heat map of multiple substitution assocaiated changes per site

Examples
multiSubChangeLoc <- system.file("extdata", "multiSubChange.rda", package = "aaSEA")
multiSubChange <- readRDS(multiSubChangeLoc)
plotMultiSubChange(multiSubChangeDF = multiSubChange )

plotSingleSubChange Plots single substitution change histogram

Description
Plots single substitution change histogram

Usage
plotSingleSubChange(singleSubChangeDF)

Arguments
singleSubChangeDF
A data frame of single amino acid substitutions per site calculated with ’getAA-
Sub’ and associated property changes obtained by calling ’getPropChange’ func-
tion
12 startSeaShiny

Value
An interactive histogram representing amino acid substitution associaited change

Examples
singleSubChangeLoc <- system.file("extdata", "singleSubChange.rda", package = "aaSEA")
singleSubChange <- readRDS(singleSubChangeLoc)
plotSingleSubChange(singleSubChangeDF = singleSubChange)

startSeaShiny Title Enables to start and run the app

Description
Title Enables to start and run the app

Usage
startSeaShiny()

Value
a shiny app will be launched in browser

Examples
if(interactive()){
startSeaShiny()
}
Index

∗Topic datasets
AAindex, 2
corSubFile, 3
Cruciani, 3
Fasgai, 4
Kidera, 8

AAindex, 2

corSubFile, 3
Cruciani, 3

Fasgai, 4

getAASub, 4
getCorPropChange, 5
getCorSites, 5
getPropChange, 6
getPropCorr, 7
getTopSub, 7

Kidera, 8

matEncode, 9

plotCorNet, 9
plotCorSubChanges, 10
plotMultiSubChange, 11
plotSingleSubChange, 11

startSeaShiny, 12

13