newLowMACA: Construct a LowMACA object

In ste-depo/LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Construct a LowMACA object

Description

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

Usage

newLowMACA(genes = NULL, pfam = NULL)

Arguments

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

Details

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.

Value

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

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

lmParams parallelize

Examples

#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)

ste-depo/LowMACA documentation built on Oct. 15, 2022, 11:53 p.m.