newLowMACA: Construct a LowMACA object
In LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

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

Constructor for the class LowMACA. It initializes a LowMACA object with default parameters

1	newLowMACA(genes = NULL, pfam = NULL)

`genes`	a character vector of gene symbols in HGNC format or a integer vector of Entrez IDs. If `pfam` is defined, it can be set to NULL
`pfam`	a character vector of pfam IDs. If `genes` is defined, it can be set to NULL

When a LowMACA object is initialized, the arguments slot is filled with the input data and default parameters and path to clustalomega aligner. See lmParams and parallelize to change them.

An object of class "LowMACA". See LowMACA-class

Stefano de Pretis , Giorgio Melloni

lmParams parallelize

#Set Genes and pfam for the analysis
Genes <- c("ADNP","ALX1","ALX4","ARGFX","CDX4","CRX"
    	,"CUX1","CUX2","DBX2","DLX5","DMBX1","DRGX"
			,"DUXA","ESX1","EVX2","HDX","HLX","HNF1A"
			,"HOXA1","HOXA2","HOXA3","HOXA5","HOXB1","HOXB3"
			,"HOXD3","ISL1","ISX","LHX8")
Pfam <- "PF00046"
#LowMACA object of pfam PF00046 filtered by Genes
lm <- newLowMACA(genes=Genes , pfam=Pfam)
#LowMACA object of the entire pfam PF00046
lm <- newLowMACA(pfam=Pfam)
#LowMACA object of entire canonical proteins associated to Genes
lm <- newLowMACA(genes=Genes)