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 3.7.2 Index]