mandatory_IS_vars: Current dynamic vars specifications getters.

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Current dynamic vars specifications getters.

Description

Fetches the look-up tables for different categories of dynamic vars. For more details, refer to the dedicated vignette vignette("workflow_start", package="ISAnalytics").

• mandatory_IS_vars returns the look-up table of variables that are used to uniquely identify integration events

• annotation_IS_vars() returns the look-up table of variables that contain genomic annotations

• association_file_columns() returns the look-up table of variables that contains information on how metadata is structured

• iss_stats_specs() returns the look-up table of variables that contains information on the format of pool statistics files produced automatically by VISPA2

• matrix_file_suffixes() returns the look-up table of variables that contains all default file names for each quantification type and it is used by automated import functions

Usage

mandatory_IS_vars(include_types = FALSE)

annotation_IS_vars(include_types = FALSE)

association_file_columns(include_types = FALSE)

iss_stats_specs(include_types = FALSE)

matrix_file_suffixes()

Arguments

include_types

If set to TRUE returns both the names and the types associated, otherwise returns only a character vector of names

Value

A character vector or a data frame

See Also

Other dynamic vars: inspect_tags(), pcr_id_column(), reset_mandatory_IS_vars(), set_mandatory_IS_vars(), set_matrix_file_suffixes()

Examples

# Names only
mandatory_IS_vars()

# Names and types
mandatory_IS_vars(TRUE)

# Names only
annotation_IS_vars()

# Names and types
annotation_IS_vars(TRUE)

# Names only
association_file_columns()

# Names and types
association_file_columns(TRUE)

# Names only
iss_stats_specs()

# Names and types
iss_stats_specs(TRUE)

# Names only
matrix_file_suffixes()

calabrialab/ISAnalytics documentation built on Nov. 2, 2023, 8:57 p.m.