set_matrix_file_suffixes: Sets the look-up table for matrix file suffixes.

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

Sets the look-up table for matrix file suffixes.

Description

The function automatically produces and sets a look-up table of matrix file suffixes based on user input.

Usage

set_matrix_file_suffixes(
  quantification_suffix = list(seqCount = "seqCount", fragmentEstimate =
    "fragmentEstimate", barcodeCount = "barcodeCount", cellCount = "cellCount", ShsCount
    = "ShsCount"),
  annotation_suffix = list(annotated = ".no0.annotated", not_annotated = ""),
  file_ext = "tsv.gz",
  glue_file_spec = "{quantification_suffix}_matrix{annotation_suffix}.{file_ext}"
)

Arguments

quantification_suffix	A named list - names must be quantification types in quantification_types(), and values must be single strings, containing the associated suffix. Please note that ALL quantification types must be specified or the function will produce an error.
annotation_suffix	A named list - names must be annotated and not_annotated, values must be single strings, containing the associated suffix. Please note that both names must be present in the list or the function will produce an error.
file_ext	The file extension (e.g. tsv, tsv.gz)
glue_file_spec	A string specifying the pattern used to form the entire suffix, as per glue::glue() requirements. The string should contain the reference to quantification_suffix, annotation_suffix and file_ext.

Value

NULL

See Also

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

Examples

set_matrix_file_suffixes(
    quantification_suffix = list(
        seqCount = "sc",
        fragmentEstimate = "fe",
        barcodeCount = "barcodeCount",
        cellCount = "cellCount",
        ShsCount = "ShsCount"
    ),
    annotation_suffix = list(annotated = "annot", not_annotated = "")
)
matrix_file_suffixes()
reset_matrix_file_suffixes()

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