writeAsymmetricMeltedChromosomalMatrixToDisk {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.

Usage

writeAsymmetricMeltedChromosomalMatrixToDisk(
  whole_genome_matrix,
  chrom1,
  chrom2,
  extra_data_matrix = NULL,
  transpose = F,
  sequential = T,
  debug = T,
  desired_range_start = 50,
  desired_range_end = 300,
  saveToDisk = T,
  max_cap = NULL,
  rescale = T
)

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).

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 parallelization with registerDoSEQ()?

debug

extra output

desired_range_start

start of range for width and height of matrix for downsampling

desired_range_end

end of range for width and height of matrix for downsampling

saveToDisk

saves the matrix to disk

max_cap

maximum saturation cap, passed to signedRescale

rescale

perform signedRescale() on matrix?

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"))
writeAsymmetricMeltedChromosomalMatrixToDisk(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")