searchPublished: Search for T cell receptor beta CDR3 amino acid sequences...
In elulu3/LymphoSeqTest: Analyze high-throughput sequencing of T and B cell receptors
View source: R/searchPublished.R
searchPublished R Documentation
Search for T cell receptor beta CDR3 amino acid sequences with known antigen
specificity
Description
Search for published T cell receptor beta CDR3 amino acid sequences with
known antigen specificity in a list of data frames.
Usage
searchPublished(study_table)
Arguments
study_table
A tibble generated by the LymphoSeq functions
readImmunoSeq or productiveSeq. "junction_aa", "frequencyCount", and "count"
are required columns.
Value
Returns a data frame of each repertoire_id name and instance in the repertoire_id
that the published TCR sequence appeared along with additional
information including antigen specificity, epitope, HLA type, and PubMed ID
(PMID) for the reference where the sequence was characterized. The
publishedTRB database is located in a separate package called LymphoSeqDB
that should be loaded automatically.
See Also
Refer to the LymphoSeqDB package for details regarding the
publishedTRB database.
elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.
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View source: R/searchPublished.R
| searchPublished | R Documentation |
Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity
Description
Search for published T cell receptor beta CDR3 amino acid sequences with known antigen specificity in a list of data frames.
Usage
searchPublished(study_table)
Arguments
study_table |
A tibble generated by the LymphoSeq functions readImmunoSeq or productiveSeq. "junction_aa", "frequencyCount", and "count" are required columns. |
Value
Returns a data frame of each repertoire_id name and instance in the repertoire_id that the published TCR sequence appeared along with additional information including antigen specificity, epitope, HLA type, and PubMed ID (PMID) for the reference where the sequence was characterized. The publishedTRB database is located in a separate package called LymphoSeqDB that should be loaded automatically.
See Also
Refer to the LymphoSeqDB package for details regarding the publishedTRB database.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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