generate_cluster_ploidy_df: generate a dataframe with segments coordinates and...
In Militeee/rcongas: Copy Number Alterations genotyping from single-cell multiomics

generate_cluster_ploidy_df

R Documentation

generate a dataframe with segments coordinates and corresponding ploidy values for the specified number of clusters.

Description

generate a dataframe with segments coordinates and corresponding ploidy values for the specified number of clusters.

Usage

generate_cluster_ploidy_df(
  K = 2,
  spots = 5,
  probs = c(0, 1, 0, 0),
  div_factor_dist = 1e+06,
  random = TRUE,
  changes = list(`0` = c(1, 2), `1` = c(1), `2` = c(-1, 1), `3` = c(-1, 1), `4` = c(-1,
    1), `5` = c(-1), `6` = c(-1)),
  fine = FALSE,
  karyo = 1:4,
  type = "parent",
  non_random_spots = c(17, 18),
  spots_deletion = c(17, 18),
  spots_insertions = c(8),
  spots_O = c(),
  tree = generate_random_tree(K),
  segments = divide_genome_in_segments(),
  baf = TRUE
)

Arguments

`K`	integer, number of clusters to simulate
`spots`	number of segment to change when using random mode
`probs`	probabilities of picking a given CN value from the karyotype, needs to have length = length(karyo)
`random`	shold the mutated segments among parent-child subclones be choosen at random?
`changes`	what are th allowed changes in ploidy between parent-child subclnes when fine = FALSE
`fine`	allow a finer controll on the different segments
`karyo`	integer vector, alloed CN values
`type`	one of c("parent", "random"), indicates if the clusters have an evolutionary relionship or they are unrelated
`non_random_spots`	if random = FALSE, wihch spotss should harbor a mutation?
`spots_deletion`	segments where we want to insert a single chromosome deletion
`spots_O`	segments where we wanto to insert a double chromosome deletion
`tree`	a data frame with two columns, the first with the index of each cluster and the second with its parent
`spots_insertion`	segments where we want to insert a single or double (randomly sampled) chromose amplification
`approx_length`	approximate segment length