Description Usage Arguments Value Examples

View source: R/writeMeltedChromosomalMatrixToDisk.R

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

1 2 3 | ```
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)
``` |

`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 |

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

1 2 3 4 5 6 | ```
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")
``` |

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