getAnnotationMatrix {CNVScope}

Get the genes in the genomic ranges indicated by the row and column labels.

Description

Gets the genes in the ranges within each cell of the matrix.

Usage

getAnnotationMatrix(
  genomic_matrix,
  prot_only = T,
  sequential = F,
  flip_row_col = F
)

Arguments

genomic_matrix

A matrix with row and column names of the format chr1_100_200 (chr,start,end)

prot_only

Inlcude only the protein coding genes from ensembl?

sequential

Turn off parallelism with doParallel?

flip_row_col

Give column genes along the rows and row genes down columns?

Value

concatenated_gene_matrix A matrix with row and column genes

Examples

load(system.file("extdata","nbl_result_matrix_sign_small.rda",package = "CNVScope")) 
load(system.file("extdata","ensembl_gene_tx_table_prot.rda",package = "CNVScope"))
load(system.file("extdata","grch37.rda",package = "CNVScope"))
getAnnotationMatrix(genomic_matrix=nbl_result_matrix_sign_small[1:5,1:5],sequential=TRUE,
prot_only=TRUE)