commonSeqs: Common sequences in two or more samples

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

Description

Creates a data frame of the common sequences in two or more samples, reporting their frequencies in each.

Usage

commonSeqs(samples, productive.aa)

Arguments

samples	A character vector of two or more sample names in productive.aa.
productive.aa	A list of productive amino acid sequences generated by the LymphoSeq function productiveSeq where aggregate = "aminoAcid".

Value

Returns a data frame of the common sequences between two or more files displaying their frequencies in each.

See Also

commonSeqsVenn

Examples

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

file.list <- readImmunoSeq(path = file.path)

productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")

commonSeqs(samples = c("TRB_Unsorted_0", "TRB_Unsorted_32"), 
   productive.aa = productive.aa)

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