alignSequences: Align sequences via clustalo
In gmelloni/LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment
Description
Usage
Arguments
Details
Value
Warning
Author(s)
References
See Also
Examples
Description
Align sequences for an object of class LowMACA
Usage
1
2
alignSequences(object, clustalo_filename=NULL , mail=NULL ,
perlCommand="perl", use_hmm=FALSE, datum=FALSE)
Arguments
object
an object of class LowMACA containing at least 2 sequences.
clustalo_filename
a character string that contains the file name where
clustal omega alignment file will be stored. In case it's NULL
no file will be written. Default=NULL
mail
a character string indicating the email address
where error report should be sent in web mode
perlCommand
a character string containing the path to Perl executable.
if missing, "perl" will be used as default
use_hmm
When analysing Pfam sequences, it is possible to
use the Hidden Markov Model (HMM) of the
specific Pfam to align the sequences.
Default is FALSE.
datum
When analysing Pfam sequences, use all the genes
that belong to the Pfam to generate the
alignment. This creates a unique mapping between
individual residues and consensus sequence,
disregarding the set of sequences that are
selected for the analysis.
Default is FALSE.
Details
This method launches a system call to clustalo aligner
and optionally creates a fasta file in clustal format.
A warning is returned if at least one sequence has a pairwise similarity below
20% to any other sequence.
If only one sequence is passed to alignSequences, the alignment will be skipped,
but no warning will be raised.
If mail is not NULL, a local installation of clustal omega
is no longer required and the alignment is
performed using clustal omega EBI web service. A limit of 2000 sequences is set
in this case and perl must be installed in the system
Value
The method returns an object of class LowMACA updating the slot alignment.
See lmAlignment
Warning
When a sequence has a similarity below 20%, a warning is raised. In order to produce strong results
in terms of conservation of multiple mutations, consider to remove that sequence
from the analysis. The alignment will obviously change.
Author(s)
Stefano de Pretis, Giorgio Melloni
References
Trident Score
Clustal Omega
Clustal Omega Web Service
See Also
getMutations , mapMutations , setup
Examples
1
2
3
4
5
6
7
8
9
10
#Create an object of class LowMACA for RAS domain family
lm <- newLowMACA(pfam="PF00071" , genes=c("KRAS" , "NRAS" , "HRAS"))
#Align sequences using local installation of clustalo
lm <- alignSequences(lm)
#Web service clustalomega aligner
lm <- alignSequences(lm , mail="lowmaca@gmail.com")
#Use HMM to align
lm <- alignSequences(lm , use_hmm=TRUE)
#Use "datum"
lm <- alignSequences(lm , datum=TRUE)
gmelloni/LowMACA documentation built on May 24, 2019, 5:03 a.m.
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Description Usage Arguments Details Value Warning Author(s) References See Also Examples
Description
Align sequences for an object of class LowMACA
Usage
1 2 | alignSequences(object, clustalo_filename=NULL , mail=NULL ,
perlCommand="perl", use_hmm=FALSE, datum=FALSE)
|
Arguments
object |
an object of class LowMACA containing at least 2 sequences. |
clustalo_filename |
a character string that contains the file name where clustal omega alignment file will be stored. In case it's NULL no file will be written. Default=NULL |
mail |
a character string indicating the email address where error report should be sent in web mode |
perlCommand |
a character string containing the path to Perl executable. if missing, "perl" will be used as default |
use_hmm |
When analysing Pfam sequences, it is possible to use the Hidden Markov Model (HMM) of the specific Pfam to align the sequences. Default is FALSE. |
datum |
When analysing Pfam sequences, use all the genes that belong to the Pfam to generate the alignment. This creates a unique mapping between individual residues and consensus sequence, disregarding the set of sequences that are selected for the analysis. Default is FALSE. |
Details
This method launches a system call to clustalo aligner
and optionally creates a fasta file in clustal format.
A warning is returned if at least one sequence has a pairwise similarity below
20% to any other sequence.
If only one sequence is passed to alignSequences, the alignment will be skipped,
but no warning will be raised.
If mail is not NULL, a local installation of clustal omega
is no longer required and the alignment is
performed using clustal omega EBI web service. A limit of 2000 sequences is set
in this case and perl must be installed in the system
Value
The method returns an object of class LowMACA updating the slot alignment.
See lmAlignment
Warning
When a sequence has a similarity below 20%, a warning is raised. In order to produce strong results in terms of conservation of multiple mutations, consider to remove that sequence from the analysis. The alignment will obviously change.
Author(s)
Stefano de Pretis, Giorgio Melloni
References
Trident Score Clustal Omega Clustal Omega Web Service
See Also
getMutations , mapMutations , setup
Examples
1 2 3 4 5 6 7 8 9 10 | #Create an object of class LowMACA for RAS domain family
lm <- newLowMACA(pfam="PF00071" , genes=c("KRAS" , "NRAS" , "HRAS"))
#Align sequences using local installation of clustalo
lm <- alignSequences(lm)
#Web service clustalomega aligner
lm <- alignSequences(lm , mail="lowmaca@gmail.com")
#Use HMM to align
lm <- alignSequences(lm , use_hmm=TRUE)
#Use "datum"
lm <- alignSequences(lm , datum=TRUE)
|
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