gene.aggregate: combine genes w/equal frequency to be only once

Description Usage Arguments Details Value Examples

View source: R/gene.aggregate.R

Description

This is a helper function to process the binary or ternary matrix. Because gene data is interpolated from the bin data, linked loci within a bin will be duplicated. Duplicate frequencies create infinite combinations in the trees in infSCITE.

Usage

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Arguments

Z

binary incidence matrix or G genotype matrix. Internally, both Z or G will be turned into a Z matrics for frequency calculations.

Details

This function checks if two rows have are identical and merges them into one. It also creates unique rownames to know what was de-duplicated

Value

returns a de-duplicated incidence or ternary matrix with rownams naving the multipe duplicated rows

Examples

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## Not run: 
data(cnr)

## for binary data
Z <- binary.cnr(cnr$genes[, c("CDK4", "MDM2", "HMGA2")])

aggrMat.Z <- gene.aggregate(Z = Z)

## for ternary data
G <- ternary.cnr(cnr$genes[, c("CDK4", "MDM2", "HMGA2")])

aggrMat.G <- gene.aggregate(Z = G)

## End(Not run)

SingerLab/gac documentation built on July 22, 2021, 3:27 a.m.