writeMeltedChromosomalMatrixToDisk {CNVScope}

Write a matrix, with genes, of a submatrix of a whole genome interaction matrix to disk.

Description

Writes an RData file with a ggplot2 object within the current directory.

Usage

writeMeltedChromosomalMatrixToDisk(
  whole_genome_matrix,
  chrom1,
  chrom2,
  filename,
  extra_data_matrix = NULL,
  transpose = F,
  sequential = T,
  debug = T,
  desired_range_start = 50,
  desired_range_end = 300
)

Arguments

whole_genome_matrix

A matrix to have edges averaged with genomic coordinates in the form chr1_50_100 set as the column and row names.

chrom1

first chromosome of the two which will subset the matrix. (this is done in row-column fasion).

chrom2

second chromosome of the two which will subset the matrix. (this is done in row-column fasion).

filename

the filename to be written

extra_data_matrix

A matrix with additional variables about each point, one position per row with as many variables as remaining columns.

transpose

transpose the matrix?

sequential

Disable paralleization with doParallel? registerDoSEQ() is used for this.

debug

verbose output for debugging

desired_range_start

the downsampled matrix must be of this size (rows & cols) at minimum

desired_range_end

the downsampled matrix must be of this size (rows & cols) at maximum

Value

ggplotmatrix a matrix with values sufficient to create a ggplot2 heatmap with geom_tile() or with ggiraph's geom_tile_interactive()

Examples

load(system.file("extdata","grch37.rda",package = "CNVScope"))
load(system.file("extdata","nbl_result_matrix_sign_small.rda",package = "CNVScope"))
load(system.file("extdata","ensembl_gene_tx_table_prot.rda",package = "CNVScope"))
writeMeltedChromosomalMatrixToDisk(whole_genome_matrix = nbl_result_matrix_sign_small,
chrom1 = 1,chrom2 = 1,desired_range_start = 25, desired_range_end = 25)
file.remove("chr1_chr1_melted.RData")