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_varsreturns 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
TRUEreturns both the names and the types associated, otherwise returns only a character vector of names
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()
#> [1] "chr" "integration_locus" "strand"
# Names and types
mandatory_IS_vars(TRUE)
#> # A tibble: 3 × 5
#> names types transform flag tag
#> <chr> <chr> <list> <chr> <chr>
#> 1 chr char <NULL> required chromosome
#> 2 integration_locus int <NULL> required locus
#> 3 strand char <NULL> required is_strand
# Names only
annotation_IS_vars()
#> [1] "GeneName" "GeneStrand"
# Names and types
annotation_IS_vars(TRUE)
#> # A tibble: 2 × 5
#> names types transform flag tag
#> <chr> <chr> <list> <chr> <chr>
#> 1 GeneName char <NULL> required gene_symbol
#> 2 GeneStrand char <NULL> required gene_strand
# Names only
association_file_columns()
#> [1] "ProjectID" "FUSIONID"
#> [3] "PoolID" "TagSequence"
#> [5] "SubjectID" "VectorType"
#> [7] "VectorID" "ExperimentID"
#> [9] "Tissue" "TimePoint"
#> [11] "DNAFragmentation" "PCRMethod"
#> [13] "TagIDextended" "Keywords"
#> [15] "CellMarker" "TagID"
#> [17] "NGSProvider" "NGSTechnology"
#> [19] "ConverrtedFilesDir" "ConverrtedFilesName"
#> [21] "SourceFileFolder" "SourceFileNameR1"
#> [23] "SourceFileNameR2" "DNAnumber"
#> [25] "ReplicateNumber" "DNAextractionDate"
#> [27] "DNAngUsed" "LinearPCRID"
#> [29] "LinearPCRDate" "SonicationDate"
#> [31] "LigationDate" "1stExpoPCRID"
#> [33] "1stExpoPCRDate" "2ndExpoID"
#> [35] "2ndExpoDate" "FusionPrimerPCRID"
#> [37] "FusionPrimerPCRDate" "PoolDate"
#> [39] "SequencingDate" "VCN"
#> [41] "Genome" "SequencingRound"
#> [43] "Genotype" "TestGroup"
#> [45] "MOI" "Engraftment"
#> [47] "Transduction" "Notes"
#> [49] "AddedField1" "AddedField2"
#> [51] "AddedField3" "AddedField4"
#> [53] "concatenatePoolIDSeqRun" "AddedField6_RelativeBloodPercentage"
#> [55] "AddedField7_PurityTestFeasibility" "AddedField8_FacsSeparationPurity"
#> [57] "Kapa" "ulForPool"
#> [59] "CompleteAmplificationID" "UniqueID"
#> [61] "StudyTestID" "StudyTestGroup"
#> [63] "MouseID" "Tigroup"
#> [65] "Tisource" "PathToFolderProjectID"
#> [67] "SamplesNameCheck" "TimepointDays"
#> [69] "TimepointMonths" "TimepointYears"
#> [71] "ng DNA corrected"
# Names and types
association_file_columns(TRUE)
#> # A tibble: 71 × 5
#> names types transform flag tag
#> <chr> <chr> <list> <chr> <chr>
#> 1 ProjectID char <NULL> required project_id
#> 2 FUSIONID char <NULL> optional fusion_id
#> 3 PoolID char <NULL> required pool_id
#> 4 TagSequence char <NULL> required tag_seq
#> 5 SubjectID char <NULL> required subject
#> 6 VectorType char <NULL> optional NA
#> 7 VectorID char <NULL> required vector_id
#> 8 ExperimentID char <NULL> optional NA
#> 9 Tissue char <NULL> required tissue
#> 10 TimePoint char <formula> required tp_days
#> # ℹ 61 more rows
# Names only
iss_stats_specs()
#> [1] "RUN_NAME" "POOL" "TAG"
#> [4] "RAW_READS" "QUALITY_PASSED" "PHIX_MAPPING"
#> [7] "PLASMID_MAPPED_BYPOOL" "BARCODE_MUX" "LTR_IDENTIFIED"
#> [10] "TRIMMING_FINAL_LTRLC" "LV_MAPPED" "BWA_MAPPED_OVERALL"
#> [13] "ISS_MAPPED_OVERALL" "ISS_MAPPED_PP"
# Names and types
iss_stats_specs(TRUE)
#> # A tibble: 14 × 5
#> names types transform flag tag
#> <chr> <chr> <list> <chr> <chr>
#> 1 RUN_NAME char <NULL> required NA
#> 2 POOL char <NULL> required vispa_concatenate
#> 3 TAG char <formula> required tag_seq
#> 4 RAW_READS int <NULL> optional NA
#> 5 QUALITY_PASSED int <NULL> optional NA
#> 6 PHIX_MAPPING int <NULL> optional NA
#> 7 PLASMID_MAPPED_BYPOOL int <NULL> optional NA
#> 8 BARCODE_MUX int <NULL> required NA
#> 9 LTR_IDENTIFIED int <NULL> optional NA
#> 10 TRIMMING_FINAL_LTRLC int <NULL> optional NA
#> 11 LV_MAPPED int <NULL> optional NA
#> 12 BWA_MAPPED_OVERALL int <NULL> optional NA
#> 13 ISS_MAPPED_OVERALL int <NULL> optional NA
#> 14 ISS_MAPPED_PP int <NULL> optional NA
# Names only
matrix_file_suffixes()
#> # A tibble: 10 × 3
#> quantification matrix_type file_suffix
#> <chr> <chr> <chr>
#> 1 seqCount annotated seqCount_matrix.no0.annotated.tsv.gz
#> 2 seqCount not_annotated seqCount_matrix.tsv.gz
#> 3 fragmentEstimate annotated fragmentEstimate_matrix.no0.annotated.tsv.gz
#> 4 fragmentEstimate not_annotated fragmentEstimate_matrix.tsv.gz
#> 5 barcodeCount annotated barcodeCount_matrix.no0.annotated.tsv.gz
#> 6 barcodeCount not_annotated barcodeCount_matrix.tsv.gz
#> 7 cellCount annotated cellCount_matrix.no0.annotated.tsv.gz
#> 8 cellCount not_annotated cellCount_matrix.tsv.gz
#> 9 ShsCount annotated ShsCount_matrix.no0.annotated.tsv.gz
#> 10 ShsCount not_annotated ShsCount_matrix.tsv.gz