gGnome.js: Generate a gGnome.js instance

In mskilab/gGnome: gGnome: reference based assembly graph for analyzing rearranged genomes

Generate a gGnome.js instance

Description

Takes a table with paths to gGraphs and coverage files (optional) and generates an instance of a gGnome.js directory that is ready to visualize using gGnome.js

Usage

gGnome.js(
  data,
  name.col = "sample",
  outdir = "./gGnome.js",
  reference = "hg19",
  cov.col = "coverage",
  gg.col = "graph",
  append = FALSE,
  cov.field = "ratio",
  cov.field.col = NA,
  cov.bin.width = 10000,
  overwrite = FALSE,
  annotation = c("simple", "bfb", "chromoplexy", "chromothripsis", "del", "dm", "dup",
    "pyrgo", "qrdel", "qrdup", "qrp", "rigma", "tic", "tyfonas"),
  kag.col = "kag",
  ncn.gr = NA,
  mc.cores = 1
)

Arguments

data	either a path to a TSV/CSV or a data.table
name.col	column name in the input data table containing the sample names (default: "sample")
outdir	the path where to save the files. This path should not exist, unless you want to add more files to an existing directory in which case you must use append = TRUE
reference	name of the reference genome used. You can use one of the built-in references (hg19, hg38), or provide a path to a folder with properly formatted genes.json and metadata.json files
cov.col	column name in the input data table containing the paths to coverage files
gg.col	column name in the input data table containing the paths to RDS files containing the gGnome objects
append	if set to FALSE the the directory is expected not to exist yet (default: TRUE). By default, samples would be appended to a gGnome.js instance if the directory already exists
cov.field	the name of the field in the coverage GRanges that should be used (default: "ratio")
cov.field.col	column name in the input data table containing the name of the field in the coverage GRanges that should be used. If this is supplied then it overrides the value in "cov.field". Use this if some of your coverage files differ in the field used.
cov.bin.width	bin width to use when rebinning the coverage data (default: 1e4). If you don't want rebinning to be performed then set to NA.
overwrite	by default only files that are missing will be created. If set to TRUE then existing coverage arrow files and gGraph JSON files will be overwritten
annotation	which node/edge annotation fields to add to the gGraph JSON file. By default we assume that gGnome::events has been executed and we add the following SV annotations: 'simple', 'bfb', 'chromoplexy', 'chromothripsis', 'del', 'dm', 'dup', 'pyrgo', 'qrdel', 'qrdup', 'qrp', 'rigma', 'tic', 'tyfonas'
mc.cores	how many cores to use
ref	the genome reference name used for this dataset. This reference name must be defined in the settings.json file. By default gGnome.js accepts one of the following: hg19, hg38, covid19. If you are using a different reference then you must first add it to the settings.json file.

mskilab/gGnome documentation built on May 8, 2024, 4:25 p.m.