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 <[email protected]>
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
