getAnnotationMatrix: Get the genes in the genomic ranges indicated by the row and...

In jamesdalg/CNVScope: A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization

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)

jamesdalg/CNVScope documentation built on Aug. 18, 2022, 4:43 p.m.