readImmunoSeq: Read ImmunoSeq files

In LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description

Imports tab-separated value (.tsv) files exported by the Adaptive Biotechnologies ImmunoSEQ analyzer and stores them as a list of data frames.

Usage

readImmunoSeq(path, columns = c("aminoAcid", "nucleotide", "count",
  "count (templates)", "count (reads)", "count (templates/reads)",
  "frequencyCount", "frequencyCount (%)", "estimatedNumberGenomes",
  "vFamilyName", "dFamilyName", "jFamilyName", "vGeneName", "dGeneName",
  "jGeneName"), recursive = FALSE)

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.
columns	Column names from the tab-delimited files that you desire to import, all others will be disregarded. May use "all" to import all columns. A warning may be called if columns contain no data or must be coereced to a different class. Usually this warning can be ignored.
recursive	A Boolean value indicating whether tab-delimited files in subdirectories should be imported. If TRUE, then all files in the parent as well as the subdirectory are imported. If FALSE, then only files in the parent directory are imported.

Details

May import tab-delimited files containing antigen receptor sequencing from other sources (e.g. miTCR or miXCR) as long as the column names are the same as used by ImmunoSEQ files. Available column headings in ImmunoSEQ files are: "nucleotide", "aminoAcid", "count", "count (templates)", "count (reads)", "count (templates/reads)", "frequencyCount", "frequencyCount (%)", "cdr3Length", "vMaxResolved", "vFamilyName", "vGeneName", "vGeneAllele", "vFamilyTies", "vGeneNameTies", "vGeneAlleleTies", "dMaxResolved", "dFamilyName", "dGeneName", "dGeneAllele", "dFamilyTies", "dGeneNameTies", "dGeneAlleleTies", "jMaxResolved", "jFamilyName", "jGeneName", "jGeneAllele", "jFamilyTies", "jGeneNameTies", "jGeneAlleleTies", "vDeletion", "d5Deletion", "d3Deletion", "jDeletion", "n2Insertion", "n1Insertion", "vIndex", "n2Index", "dIndex", "n1Index", "jIndex", "estimatedNumberGenomes", "sequenceStatus", "cloneResolved", "vOrphon", "dOrphon", "jOrphon", "vFunction", "dFunction", "jFunction", "fractionNucleated".

IMPORTANT: be aware that Adaptive has changed the column names of their files over time and if the headings of your files are inconsistent, then specify column = "all" or include all variations of the headings you want to important. For example, column = c("count", "count (templates)", "count (reads)"). Also be aware that the "count" column previously reported the number of sequencing reads in earlier versions of ImmunoSEQ but now is equivalent to the "estimatedNumberGenomes" column.

Value

Returns a list of data frames. The names of each data frame are assigned according to the original ImmunoSEQ file names.

Examples

file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path, 
                           columns = c("aminoAcid", "nucleotide", "count", 
                                     "count (templates)", "count (reads)", 
                                     "count (templates/reads)",
                                     "frequencyCount", "frequencyCount (%)", 
                                     "estimatedNumberGenomes"), 
                           recursive = FALSE)

Example output

Loading required package: LymphoSeqDB
Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
sh: 1: wc: Permission denied
Could not detect number of cores, defaulting to 1.

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LymphoSeq documentation built on Nov. 8, 2020, 8:09 p.m.