DiNAMIC.Duo (version 1.0.4)

dataPrep: Prepare copy number data for downstream analysis

Description

Prepare copy number data for downstream analysis

Usage

dataPrep(
  X,
  Y = NULL,
  species = c("human", "mouse"),
  ensemblHost = "https://aug2020.archive.ensembl.org"
)

Value

a list of processed X and Y with a data frame containing gene annotation information.

Arguments

X

a matrix or a data frame of copy number data. The rows and columns of X correspond to genes and subjects, respectively. X must have gene symbols as its row names.

Y

an optional matrix or data frame of copy number data to compare with X. As is the case for X, the rows and columns of Y correspond to genes and subjects, respectively. Y must have gene symbols as its row names.

species

a value specifying species for ensembl database to be used; Default is "human".

ensemblHost

specifies the Ensembl archive used; Default is "http://aug2020.archive.ensembl.org".

Details

This helper function is designed to prepare input matrices or data frames X and Y containing DNA copy number data for analysis. The downstream functions that X and Y are indexed by a common set of genes that appear in genomic order. In addition, the peelingOne and peelingTwo functions require information about the cytoband for each gene, and the resultsProcess function uses information about gene position. The dataPrep function queries biomaRt so users are not required to provide this information.

Examples

# \donttest{
#This runtime for this code slightly exceeds the limits imposed by CRAN.
data(DiNAMIC.Duo)
output = dataPrep(X=luadSubset,Y=NULL)
# }