wilson (version 2.4.2)

tobias_parser: TOBIAS TFBS table to clarion parser

Description

Click here for more information about TOBIAS.

Usage

tobias_parser(
  input,
  output,
  filter_columns = NULL,
  filter_pattern = NULL,
  config = system.file("extdata", "tobias_config.json", package = "wilson"),
  omit_NA = FALSE,
  condition_names = NULL,
  condition_pattern = "_bound$",
  in_field_delimiter = ",",
  dec = ".",
  ...
)

Arguments

input

Path to input table

output

Output path.

filter_columns

Either a vector of columnnames or a file containing one columnname per row.

filter_pattern

Keep columns matching the given pattern. Uses parameter filter_columns for matching if set. In the case of no matches a warning will be issued and all columns will be used.

config

Json file containing metadata information for all columns. Will use first occurence for duplicate column names.

omit_NA

Logical whether all rows containing NA should be removed.

condition_names

Vector of condition names. Default = NULL. Used to classify columns not provided in config.

condition_pattern

Used to identify condition names by matching and removing given pattern with grep. Ignored when condition_names is set.

in_field_delimiter

Delimiter for multi value fields. Default = ','.

dec

Decimal separator. Used in file reading and writing.

...

Used as header information.

Details

During conversion the parser will try to use the given config (if provided) to create the Clarion metadata. In the case of insufficient config information it will try to approximate by referencing condition names issuing warnings in the process.

As the format requires an unique id the parser will create one if necessary.

Factor grouping (metadata factor columns) is currently not implemented!