setup: Setup of a LowMACA object
In LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Description Usage Arguments Details Value Author(s) References See Also Examples

A wrapper around alignSequences , getMutations and mapMutations in order to execute all these methods at once.

1 2	setup(object, repos = NULL, clustalo_filename=NULL , mail=NULL , perlCommand="perl", use_hmm=FALSE, datum=FALSE)

`object`	an object of class LowMACA
`repos`	a data.frame containing mutations for the specified genes in the LowMACA object in case of custom mutation data. Default NULL
`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. Default is NULL, to use a local clustalo installation
`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.

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 is required with XML::Simple and LWP modules installed

An object of class LowMACA with all the updates provided by alignSequences , getMutations and mapMutations methods.

Stefano de Pretis , Giorgio Melloni

Trident Score Clustal Omega Clustal Omega Web Service

alignSequences getMutations mapMutations

#Create an object of class LowMACA for RAS domain family
lm <- newLowMACA(pfam="PF00071" , genes=c("KRAS" , "NRAS" , "HRAS"))
#Select a few tumor types
lmParams(lm)$tumor_type <- c("skcm" , "brca" , "coadread")
#Align sequences, get mutation data and map them on consensus
lm <- setup(lm)
#Same as above, but using web service
lm <- setup(lm , mail="lowmaca@gmail.com")
#Use HMM to align
lm <- setup(lm , use_hmm=TRUE)
#Use "datum"
lm <- setup(lm , datum=TRUE)