Common sequences in two or more samples

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

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("TCRB_Day0_Unsorted", "TCRB_Day32_Unsorted"), 
   productive.aa = productive.aa)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(LymphoSeq)
Loading required package: LymphoSeqDB
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LymphoSeq/commonSeqs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: commonSeqs
> ### Title: Common sequences in two or more samples
> ### Aliases: commonSeqs
> 
> ### ** Examples
> 
> file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")
> 
> file.list <- readImmunoSeq(path = file.path)
   |                                                                               |                                                                      |   0%   |                                                                               |======                                                                |   9%   |                                                                               |=============                                                         |  18%   |                                                                               |===================                                                   |  27%   |                                                                               |=========================                                             |  36%   |                                                                               |================================                                      |  45%   |                                                                               |======================================                                |  55%   |                                                                               |=============================================                         |  64%   |                                                                               |===================================================                   |  73%   |                                                                               |=========================================================             |  82%   |                                                                               |================================================================      |  91%   |                                                                               |======================================================================| 100%
> 
> productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")
   |                                                                               |                                                                      |   0%   |                                                                               |======                                                                |   9%   |                                                                               |=============                                                         |  18%   |                                                                               |===================                                                   |  27%   |                                                                               |=========================                                             |  36%   |                                                                               |================================                                      |  45%   |                                                                               |======================================                                |  55%   |                                                                               |=============================================                         |  64%   |                                                                               |===================================================                   |  73%   |                                                                               |=========================================================             |  82%   |                                                                               |================================================================      |  91%   |                                                                               |======================================================================| 100%
> 
> commonSeqs(samples = c("TCRB_Day0_Unsorted", "TCRB_Day32_Unsorted"), 
+    productive.aa = productive.aa)
        aminoAcid TCRB_Day0_Unsorted TCRB_Day32_Unsorted
1 CASSQDRTGQYGYTF         0.47380673          0.80551900
2    CAWTGGTTEAFF         0.10887567          0.15153328
3    CAISEGNYGYTF         0.03566995          0.18742274
4   CASSFGIQETQYF         0.01393872          0.09570523
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>