Creates a data frame of the top productive amino acid sequences that have a specified minimum frequency threshold and reports the number of samples that the sequence appears in along with the minimum, maximum, and mean frequency across all samples. For T cell receptor beta sequences, the % prevalence and antigen specificity of that sequence is also provided.
topFreq(productive.aa, percent = 0.1)
A list data frames of of productive amino acid sequences imported using the function LymphoSeq function productiveSeq where the aggregate parameter was set to "aminoAcid".
The minimum % frequency that the sequence appears in any of the listed samples.
A data frame of amino acid sequences and the number of samples that the sequence appears in along with the minimum, maximum, and mean frequency across all samples. For T cell receptor beta sequences, additionally reported is the % prevalence that the sequence appears in 55 healthy donor blood samples. Also provided is the antigen specificity of that sequence if known by comparing it to a database of previously reported sequences in the literature. The prevalenceTRB and publishedTRB databases are located in a separate package called LymphoSeqDB that should be loaded automatically.
Refer to the LymphoSeqDB package for details regarding the prevalenceTRB and publishedTRB database.
1 2 3 4 5 6 7
Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.