Sets the look-up table for matrix file suffixes.

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 suffixes specs successfully changed
matrix_file_suffixes()
#> # A tibble: 10 × 3
#>    quantification   matrix_type   file_suffix                    
#>    <chr>            <chr>         <chr>                          
#>  1 seqCount         annotated     sc_matrixannot.tsv.gz          
#>  2 seqCount         not_annotated sc_matrix.tsv.gz               
#>  3 fragmentEstimate annotated     fe_matrixannot.tsv.gz          
#>  4 fragmentEstimate not_annotated fe_matrix.tsv.gz               
#>  5 barcodeCount     annotated     barcodeCount_matrixannot.tsv.gz
#>  6 barcodeCount     not_annotated barcodeCount_matrix.tsv.gz     
#>  7 cellCount        annotated     cellCount_matrixannot.tsv.gz   
#>  8 cellCount        not_annotated cellCount_matrix.tsv.gz        
#>  9 ShsCount         annotated     ShsCount_matrixannot.tsv.gz    
#> 10 ShsCount         not_annotated ShsCount_matrix.tsv.gz         
reset_matrix_file_suffixes()
#> Matrix suffixes specs reset to default