combine_dfs: Combine (and optionally process) data for one simulation
In robjohnnoble/demonanalysis: Analysis and plotting of demon data

Description Usage Arguments Details Value Examples

Combine (and optionally process) data for one simulation

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combine_dfs(full_dir, include_diversities = TRUE, df_type = "output",
  max_generation = FALSE, vaf_cut_off = NA, generation = NA,
  numcells = NA, num_parameters = NA, ExitCode4 = FALSE)

`full_dir`	base input directory name
`include_diversities`	boolean whether to include diversity metrics (if df_type == "output")
`df_type`	which dataframes to combine
`max_generation`	If TRUE then results are returned only for the final generation
`vaf_cut_off`	exclude genotypes with vaf lower than cut off (if df_type == "genotype_properties" or "driver_genotype_properties")
`generation`	Generation at which to filter (default NA corresponds to no filtering)
`numcells`	Number of cells at which to filter (default NA corresponds to no filtering)
`num_parameters`	Number of parameters, accounting for the first set of columns in the dataframe (optional, but may improve speed)
`ExitCode4`	Allow to deal with simulations including treatment. Simulations for which the tumor die at the treatment time end with "Exit Code =4", we need to deal in a specific way (i.e need to remove the lines with Treated==1) with these simulations when combining the output (as these simulations have most columns containing missing valeus/NA after the treatment).

If both generation and numcells are provided then numcells takes precedent.

the combined dataframe

combine_dfs(system.file("extdata", "", package = "demonanalysis", mustWork = TRUE))
combine_dfs(full_dir = system.file("extdata", "", package = "demonanalysis", mustWork = TRUE), 
df_type = "driver_genotype_properties")
combine_dfs(full_dir = system.file("extdata", "", package = "demonanalysis", mustWork = TRUE), 
df_type = "genotype_properties", vaf_cut_off = 0.002)
combine_dfs(full_dir = system.file("extdata", "", package = "demonanalysis", mustWork = TRUE), 
df_type = "genotype_counts", numcells = 100)