getAnnotationMatrix {CNVScope}R Documentation

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)

[Package CNVScope version 3.6.0 Index]