newLowMACA: Construct a LowMACA object

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

Description

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

Usage

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
#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)


Search within the LowMACA package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.