read_isomut_from_dir: Read isomut data from directory
In fridoling/isomutR: isomutR

Description Usage Arguments Value

Read isomut data from directory

read_isomut_from_dir(
  dir,
  minReads = 0L,
  minCoverage = 0,
  minMutFreq = 0,
  minScore = 0,
  minCleanliness = 0,
  removePatterns = NULL,
  extraColumns = NULL,
  removeFeatures = TRUE,
  featureData = SGD_features,
  removeMito = TRUE,
  verbose = TRUE,
  asDataFrame = TRUE,
  annotate = TRUE,
  ...
)

`dir`	path to the directory containing isomut data.
`minReads`	integer indicating the minimum number of reads (default = 0L).
`minCoverage`	double indicating the minimum coverage (default = 0).
`minMutFreq`	double indicating the minimum mutation frequency (default = 0).
`minScore`	double indicating the minimum isomut score (default = 0).
`minCleanliness`	double indicating the minimum isomut cleanliness (default = 0).
`removePatterns`	character vector providing patterns in sample_names that are to be removed.
`extraColumns`	named list to generate extra columns. The list names are the names of the new columns. The list elements can either be a vector of length one (each row gets the same value for this column), a named vector with names being a subset of the `sample_name` column in the original isomut file, or a function that accepts those names as arguments.
`removeFeatures`	whether certain genomic features should be removed.
`featureData`	`GRanges` that contains features to be removed.
`removeMito`	whether variants in mitochondrial DNA should be removed.
`verbose`	monitor progress.
`asDataFrame`	whether to return a `data.frame`. If `FALSE`, a `data.table` is returned.
`annotate`	whether data should be annotated. For details see `annotate_isomut`.
`...`	further arguments for `annotate_isomut`.