Imports tab-separated value (.tsv) files exported by the Adaptive Biotechnologies ImmunoSEQ analyzer, BGI IR-SEQ, MiXCR and stores them as MiAIRR compliant tibble.
Usage
readImmunoSeq(path, recursive = FALSE)
getStandard(clone_file, airr_fields, matching_fields)
readFiles(clone_file, empty_airr_frame, matching_fields, progress)
iReceptorFormat(clone_frame)Arguments
- path
Path to the directory containing tab-delimited files. Only files with the extension .tsv are imported. The names of the data frames are the same as names of the files.
- clone_file
.tsv file containing results from AIRRSeq pipeline
- airr_fields
A character vector of MiAIRR headers
- clone_frame
An AIRR compliant tibble
Value
Returns a tibble with MiAIRR headers and repertoire_id Tibble of given data with MiAIRR fields Tibble in MiAIRR format Tibble in iReceptor format
Read clone file from path
Given the path to a single AIRRSeq clone file, generate MiAIRR compliant tibble.
Get iReceptor standard format
Returns a tibble that is compliant with the iReceptor repertoire format.
Examples
file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeqTest")
study_table <- readImmunoSeq(path = file.path,
recursive = FALSE)
#> Rows: 1 Columns: 144
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (69): sequence_id, sequence, sequence_aa, locus, v_call, d_call, d2_call...
#> dbl (70): v_score, v_identity, v_support, d_score, d_identity, d_support, d2...
#> lgl (5): rev_comp, productive, vj_in_frame, stop_codon, complete_vdj
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (33): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl (4): vFamilyTies, jFamilyTies, jGeneNameTies, jGeneAlleleTies
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (34): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl (3): jFamilyTies, jGeneNameTies, jGeneAlleleTies
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 414 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (34): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl (3): jFamilyTies, jGeneNameTies, jGeneAlleleTies
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (34): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl (3): jFamilyTies, jGeneNameTies, jGeneAlleleTies
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (34): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl (3): jFamilyTies, jGeneNameTies, jGeneAlleleTies
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (35): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl (2): jFamilyTies, jGeneAlleleTies
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 920 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (29): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vFami...
#> dbl (14): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl (9): vGeneAllele, vGeneAlleleTies, dGeneAllele, dFamilyTies, dGeneAllel...
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (29): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vFami...
#> dbl (14): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl (9): vGeneAllele, vGeneAlleleTies, dGeneAllele, dFamilyTies, dGeneAllel...
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (29): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vFami...
#> dbl (14): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl (9): vGeneAllele, vGeneAlleleTies, dGeneAllele, dFamilyTies, dGeneAllel...
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")
#> Rows: 1000 Columns: 52
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (34): nucleotide, aminoAcid, vMaxResolved, vFamilyName, vGeneName, vGene...
#> dbl (15): count (templates/reads), frequencyCount (%), cdr3Length, vDeletion...
#> lgl (3): jFamilyTies, jGeneNameTies, jGeneAlleleTies
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Joining, by = c("sequence", "sequence_aa", "v_call", "d_call", "d2_call",
#> "j_call", "junction", "junction_aa", "duplicate_count", "clone_id",
#> "repertoire_id")