vignettes/articles/Processing.Rmd
Processing.RmdWhat if there are more variables to add than just sample and ID? We
can add them by using the addVariable() function. All we
need is the variable.name of the variable you’d like to
add and the specific character or numeric values
(variables). As an example, here we add the
Type in which the samples were processed and
sequenced.
combined.TCR <- addVariable(combined.TCR,
variable.name = "Type",
variables = rep(c("B", "L"), 4))
head(combined.TCR[[1]])## barcode sample TCR1 cdr3_aa1
## 1 P17B_AAACCTGAGTACGACG-1 P17B TRAV25.TRAJ20.TRAC CGCSNDYKLSF
## 3 P17B_AAACCTGCAACACGCC-1 P17B TRAV38-2/DV8.TRAJ52.TRAC CAYRSAQAGGTSYGKLTF
## 5 P17B_AAACCTGCAGGCGATA-1 P17B TRAV12-1.TRAJ9.TRAC CVVSDNTGGFKTIF
## 7 P17B_AAACCTGCATGAGCGA-1 P17B TRAV12-1.TRAJ9.TRAC CVVSDNTGGFKTIF
## 9 P17B_AAACGGGAGAGCCCAA-1 P17B TRAV20.TRAJ8.TRAC CAVRGEGFQKLVF
## 10 P17B_AAACGGGAGCGTTTAC-1 P17B TRAV12-1.TRAJ9.TRAC CVVSDNTGGFKTIF
## cdr3_nt1
## 1 TGTGGGTGTTCTAACGACTACAAGCTCAGCTTT
## 3 TGTGCTTATAGGAGCGCGCAGGCTGGTGGTACTAGCTATGGAAAGCTGACATTT
## 5 TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT
## 7 TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT
## 9 TGTGCTGTGCGAGGAGAAGGCTTTCAGAAACTTGTATTT
## 10 TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT
## TCR2 cdr3_aa2
## 1 TRBV5-1.None.TRBJ2-7.TRBC2 CASSLTDRTYEQYF
## 3 TRBV10-3.None.TRBJ2-2.TRBC2 CAISEQGKGELFF
## 5 TRBV9.None.TRBJ2-2.TRBC2 CASSVRRERANTGELFF
## 7 TRBV9.None.TRBJ2-2.TRBC2 CASSVRRERANTGELFF
## 9 <NA> <NA>
## 10 TRBV9.None.TRBJ2-2.TRBC2 CASSVRRERANTGELFF
## cdr3_nt2
## 1 TGCGCCAGCAGCTTGACCGACAGGACCTACGAGCAGTACTTC
## 3 TGTGCCATCAGTGAACAGGGGAAAGGGGAGCTGTTTTTT
## 5 TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
## 7 TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
## 9 <NA>
## 10 TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
## CTgene
## 1 TRAV25.TRAJ20.TRAC_TRBV5-1.None.TRBJ2-7.TRBC2
## 3 TRAV38-2/DV8.TRAJ52.TRAC_TRBV10-3.None.TRBJ2-2.TRBC2
## 5 TRAV12-1.TRAJ9.TRAC_TRBV9.None.TRBJ2-2.TRBC2
## 7 TRAV12-1.TRAJ9.TRAC_TRBV9.None.TRBJ2-2.TRBC2
## 9 TRAV20.TRAJ8.TRAC_NA
## 10 TRAV12-1.TRAJ9.TRAC_TRBV9.None.TRBJ2-2.TRBC2
## CTnt
## 1 TGTGGGTGTTCTAACGACTACAAGCTCAGCTTT_TGCGCCAGCAGCTTGACCGACAGGACCTACGAGCAGTACTTC
## 3 TGTGCTTATAGGAGCGCGCAGGCTGGTGGTACTAGCTATGGAAAGCTGACATTT_TGTGCCATCAGTGAACAGGGGAAAGGGGAGCTGTTTTTT
## 5 TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
## 7 TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
## 9 TGTGCTGTGCGAGGAGAAGGCTTTCAGAAACTTGTATTT_NA
## 10 TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
## CTaa
## 1 CGCSNDYKLSF_CASSLTDRTYEQYF
## 3 CAYRSAQAGGTSYGKLTF_CAISEQGKGELFF
## 5 CVVSDNTGGFKTIF_CASSVRRERANTGELFF
## 7 CVVSDNTGGFKTIF_CASSVRRERANTGELFF
## 9 CAVRGEGFQKLVF_NA
## 10 CVVSDNTGGFKTIF_CASSVRRERANTGELFF
## CTstrict
## 1 TRAV25.TRAJ20.TRAC;TGTGGGTGTTCTAACGACTACAAGCTCAGCTTT_TRBV5-1.None.TRBJ2-7.TRBC2;TGCGCCAGCAGCTTGACCGACAGGACCTACGAGCAGTACTTC
## 3 TRAV38-2/DV8.TRAJ52.TRAC;TGTGCTTATAGGAGCGCGCAGGCTGGTGGTACTAGCTATGGAAAGCTGACATTT_TRBV10-3.None.TRBJ2-2.TRBC2;TGTGCCATCAGTGAACAGGGGAAAGGGGAGCTGTTTTTT
## 5 TRAV12-1.TRAJ9.TRAC;TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TRBV9.None.TRBJ2-2.TRBC2;TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
## 7 TRAV12-1.TRAJ9.TRAC;TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TRBV9.None.TRBJ2-2.TRBC2;TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
## 9 TRAV20.TRAJ8.TRAC;TGTGCTGTGCGAGGAGAAGGCTTTCAGAAACTTGTATTT_NA;NA
## 10 TRAV12-1.TRAJ9.TRAC;TGTGTGGTCTCCGATAATACTGGAGGCTTCAAAACTATCTTT_TRBV9.None.TRBJ2-2.TRBC2;TGTGCCAGCAGCGTAAGGAGGGAAAGGGCGAACACCGGGGAGCTGTTTTTT
## Type
## 1 B
## 3 B
## 5 B
## 7 B
## 9 B
## 10 BLikewise, we can remove specific list elements after
combineTCR() using the subsetClones()
function. In order to subset, we need to identify the vector we would
like to use for subsetting (name) and the variable
values to subset (variables). Below, we isolate just
the 2 sequencing results from P18L and P18B.
subset1 <- subsetClones(combined.TCR,
name = "sample",
variables = c("P18L", "P18B"))
head(subset1[[1]])## barcode sample TCR1 cdr3_aa1
## 1 P18B_AAACCTGAGGCTCAGA-1 P18B TRAV26-1.TRAJ37.TRAC CIVRGGSSNTGKLIF
## 3 P18B_AAACCTGCATGACATC-1 P18B TRAV3.TRAJ20.TRAC CAVQRSNDYKLSF
## 5 P18B_AAACCTGGTATGCTTG-1 P18B TRAV26-1.TRAJ53.TRAC CIGSSGGSNYKLTF
## 8 P18B_AAACGGGCAGATGGGT-1 P18B <NA> <NA>
## 9 P18B_AAACGGGTCTTACCGC-1 P18B TRAV20.TRAJ9.TRAC CAVQAKRYTGGFKTIF
## 12 P18B_AAAGATGAGTTACGGG-1 P18B TRAV8-3.TRAJ8.TRAC CAVGGDTGFQKLVF
## cdr3_nt1
## 1 TGCATCGTCAGGGGCGGCTCTAGCAACACAGGCAAACTAATCTTT
## 3 TGTGCTGTGCAACGTTCTAACGACTACAAGCTCAGCTTT
## 5 TGCATCGGCTCAAGTGGAGGTAGCAACTATAAACTGACATTT
## 8 <NA>
## 9 TGTGCTGTGCAGGCCAAGCGGTATACTGGAGGCTTCAAAACTATCTTT
## 12 TGTGCTGTGGGTGGTGACACAGGCTTTCAGAAACTTGTATTT
## TCR2
## 1 TRBV6-1.None.TRBJ2-3.TRBC2
## 3 TRBV3-1.None.TRBJ2-3.TRBC2
## 5 TRBV4-1.None.TRBJ2-2.TRBC2;TRBV19.None.TRBJ1-5.TRBC1
## 8 TRBV5-1.None.TRBJ1-2.TRBC1
## 9 TRBV5-1.None.TRBJ1-1.TRBC1;TRBV7-9.None.TRBJ2-2.TRBC2
## 12 TRBV12-4.None.TRBJ1-1.TRBC1
## cdr3_aa2
## 1 CASIGRSFGRDTQYF
## 3 CASSPPRGGFTDTQYF
## 5 CASSQGGQGGRELFF;CASSYAVGRQPQHF
## 8 CASSLRETNYGYTF
## 9 CASSLGTGTGVEAFF;CAIDPGLLTGELFF
## 12 CASRNSQATEAFF
## cdr3_nt2
## 1 TGTGCCAGTATCGGGAGGTCCTTTGGCCGAGATACGCAGTATTTT
## 3 TGTGCCAGCAGCCCCCCCCGCGGCGGATTCACAGATACGCAGTATTTT
## 5 TGCGCCAGCAGCCAAGGTGGACAGGGCGGAAGGGAGCTGTTTTTT;TGTGCCAGTAGCTACGCGGTGGGGAGGCAGCCCCAGCATTTT
## 8 TGCGCCAGCAGCTTGAGGGAAACCAACTATGGCTACACCTTC
## 9 TGCGCCAGCAGCTTGGGAACGGGGACAGGGGTTGAAGCTTTCTTT;TGTGCCATCGATCCGGGACTACTCACCGGGGAGCTGTTTTTT
## 12 TGTGCCAGCAGAAACTCCCAAGCCACTGAAGCTTTCTTT
## CTgene
## 1 TRAV26-1.TRAJ37.TRAC_TRBV6-1.None.TRBJ2-3.TRBC2
## 3 TRAV3.TRAJ20.TRAC_TRBV3-1.None.TRBJ2-3.TRBC2
## 5 TRAV26-1.TRAJ53.TRAC_TRBV4-1.None.TRBJ2-2.TRBC2;TRBV19.None.TRBJ1-5.TRBC1
## 8 NA_TRBV5-1.None.TRBJ1-2.TRBC1
## 9 TRAV20.TRAJ9.TRAC_TRBV5-1.None.TRBJ1-1.TRBC1;TRBV7-9.None.TRBJ2-2.TRBC2
## 12 TRAV8-3.TRAJ8.TRAC_TRBV12-4.None.TRBJ1-1.TRBC1
## CTnt
## 1 TGCATCGTCAGGGGCGGCTCTAGCAACACAGGCAAACTAATCTTT_TGTGCCAGTATCGGGAGGTCCTTTGGCCGAGATACGCAGTATTTT
## 3 TGTGCTGTGCAACGTTCTAACGACTACAAGCTCAGCTTT_TGTGCCAGCAGCCCCCCCCGCGGCGGATTCACAGATACGCAGTATTTT
## 5 TGCATCGGCTCAAGTGGAGGTAGCAACTATAAACTGACATTT_TGCGCCAGCAGCCAAGGTGGACAGGGCGGAAGGGAGCTGTTTTTT;TGTGCCAGTAGCTACGCGGTGGGGAGGCAGCCCCAGCATTTT
## 8 NA_TGCGCCAGCAGCTTGAGGGAAACCAACTATGGCTACACCTTC
## 9 TGTGCTGTGCAGGCCAAGCGGTATACTGGAGGCTTCAAAACTATCTTT_TGCGCCAGCAGCTTGGGAACGGGGACAGGGGTTGAAGCTTTCTTT;TGTGCCATCGATCCGGGACTACTCACCGGGGAGCTGTTTTTT
## 12 TGTGCTGTGGGTGGTGACACAGGCTTTCAGAAACTTGTATTT_TGTGCCAGCAGAAACTCCCAAGCCACTGAAGCTTTCTTT
## CTaa
## 1 CIVRGGSSNTGKLIF_CASIGRSFGRDTQYF
## 3 CAVQRSNDYKLSF_CASSPPRGGFTDTQYF
## 5 CIGSSGGSNYKLTF_CASSQGGQGGRELFF;CASSYAVGRQPQHF
## 8 NA_CASSLRETNYGYTF
## 9 CAVQAKRYTGGFKTIF_CASSLGTGTGVEAFF;CAIDPGLLTGELFF
## 12 CAVGGDTGFQKLVF_CASRNSQATEAFF
## CTstrict
## 1 TRAV26-1.TRAJ37.TRAC;TGCATCGTCAGGGGCGGCTCTAGCAACACAGGCAAACTAATCTTT_TRBV6-1.None.TRBJ2-3.TRBC2;TGTGCCAGTATCGGGAGGTCCTTTGGCCGAGATACGCAGTATTTT
## 3 TRAV3.TRAJ20.TRAC;TGTGCTGTGCAACGTTCTAACGACTACAAGCTCAGCTTT_TRBV3-1.None.TRBJ2-3.TRBC2;TGTGCCAGCAGCCCCCCCCGCGGCGGATTCACAGATACGCAGTATTTT
## 5 TRAV26-1.TRAJ53.TRAC;TGCATCGGCTCAAGTGGAGGTAGCAACTATAAACTGACATTT_TRBV4-1.None.TRBJ2-2.TRBC2;TRBV19.None.TRBJ1-5.TRBC1;TGCGCCAGCAGCCAAGGTGGACAGGGCGGAAGGGAGCTGTTTTTT;TGTGCCAGTAGCTACGCGGTGGGGAGGCAGCCCCAGCATTTT
## 8 NA;NA_TRBV5-1.None.TRBJ1-2.TRBC1;TGCGCCAGCAGCTTGAGGGAAACCAACTATGGCTACACCTTC
## 9 TRAV20.TRAJ9.TRAC;TGTGCTGTGCAGGCCAAGCGGTATACTGGAGGCTTCAAAACTATCTTT_TRBV5-1.None.TRBJ1-1.TRBC1;TRBV7-9.None.TRBJ2-2.TRBC2;TGCGCCAGCAGCTTGGGAACGGGGACAGGGGTTGAAGCTTTCTTT;TGTGCCATCGATCCGGGACTACTCACCGGGGAGCTGTTTTTT
## 12 TRAV8-3.TRAJ8.TRAC;TGTGCTGTGGGTGGTGACACAGGCTTTCAGAAACTTGTATTT_TRBV12-4.None.TRBJ1-1.TRBC1;TGTGCCAGCAGAAACTCCCAAGCCACTGAAGCTTTCTTT
## Type
## 1 B
## 3 B
## 5 B
## 8 B
## 9 B
## 12 BAlternatively, we can also just select the list elements after
combineTCR() or combineBCR().
## barcode sample TCR1 cdr3_aa1
## 1 P18B_AAACCTGAGGCTCAGA-1 P18B TRAV26-1.TRAJ37.TRAC CIVRGGSSNTGKLIF
## 3 P18B_AAACCTGCATGACATC-1 P18B TRAV3.TRAJ20.TRAC CAVQRSNDYKLSF
## 5 P18B_AAACCTGGTATGCTTG-1 P18B TRAV26-1.TRAJ53.TRAC CIGSSGGSNYKLTF
## 8 P18B_AAACGGGCAGATGGGT-1 P18B <NA> <NA>
## 9 P18B_AAACGGGTCTTACCGC-1 P18B TRAV20.TRAJ9.TRAC CAVQAKRYTGGFKTIF
## 12 P18B_AAAGATGAGTTACGGG-1 P18B TRAV8-3.TRAJ8.TRAC CAVGGDTGFQKLVF
## cdr3_nt1
## 1 TGCATCGTCAGGGGCGGCTCTAGCAACACAGGCAAACTAATCTTT
## 3 TGTGCTGTGCAACGTTCTAACGACTACAAGCTCAGCTTT
## 5 TGCATCGGCTCAAGTGGAGGTAGCAACTATAAACTGACATTT
## 8 <NA>
## 9 TGTGCTGTGCAGGCCAAGCGGTATACTGGAGGCTTCAAAACTATCTTT
## 12 TGTGCTGTGGGTGGTGACACAGGCTTTCAGAAACTTGTATTT
## TCR2
## 1 TRBV6-1.None.TRBJ2-3.TRBC2
## 3 TRBV3-1.None.TRBJ2-3.TRBC2
## 5 TRBV4-1.None.TRBJ2-2.TRBC2;TRBV19.None.TRBJ1-5.TRBC1
## 8 TRBV5-1.None.TRBJ1-2.TRBC1
## 9 TRBV5-1.None.TRBJ1-1.TRBC1;TRBV7-9.None.TRBJ2-2.TRBC2
## 12 TRBV12-4.None.TRBJ1-1.TRBC1
## cdr3_aa2
## 1 CASIGRSFGRDTQYF
## 3 CASSPPRGGFTDTQYF
## 5 CASSQGGQGGRELFF;CASSYAVGRQPQHF
## 8 CASSLRETNYGYTF
## 9 CASSLGTGTGVEAFF;CAIDPGLLTGELFF
## 12 CASRNSQATEAFF
## cdr3_nt2
## 1 TGTGCCAGTATCGGGAGGTCCTTTGGCCGAGATACGCAGTATTTT
## 3 TGTGCCAGCAGCCCCCCCCGCGGCGGATTCACAGATACGCAGTATTTT
## 5 TGCGCCAGCAGCCAAGGTGGACAGGGCGGAAGGGAGCTGTTTTTT;TGTGCCAGTAGCTACGCGGTGGGGAGGCAGCCCCAGCATTTT
## 8 TGCGCCAGCAGCTTGAGGGAAACCAACTATGGCTACACCTTC
## 9 TGCGCCAGCAGCTTGGGAACGGGGACAGGGGTTGAAGCTTTCTTT;TGTGCCATCGATCCGGGACTACTCACCGGGGAGCTGTTTTTT
## 12 TGTGCCAGCAGAAACTCCCAAGCCACTGAAGCTTTCTTT
## CTgene
## 1 TRAV26-1.TRAJ37.TRAC_TRBV6-1.None.TRBJ2-3.TRBC2
## 3 TRAV3.TRAJ20.TRAC_TRBV3-1.None.TRBJ2-3.TRBC2
## 5 TRAV26-1.TRAJ53.TRAC_TRBV4-1.None.TRBJ2-2.TRBC2;TRBV19.None.TRBJ1-5.TRBC1
## 8 NA_TRBV5-1.None.TRBJ1-2.TRBC1
## 9 TRAV20.TRAJ9.TRAC_TRBV5-1.None.TRBJ1-1.TRBC1;TRBV7-9.None.TRBJ2-2.TRBC2
## 12 TRAV8-3.TRAJ8.TRAC_TRBV12-4.None.TRBJ1-1.TRBC1
## CTnt
## 1 TGCATCGTCAGGGGCGGCTCTAGCAACACAGGCAAACTAATCTTT_TGTGCCAGTATCGGGAGGTCCTTTGGCCGAGATACGCAGTATTTT
## 3 TGTGCTGTGCAACGTTCTAACGACTACAAGCTCAGCTTT_TGTGCCAGCAGCCCCCCCCGCGGCGGATTCACAGATACGCAGTATTTT
## 5 TGCATCGGCTCAAGTGGAGGTAGCAACTATAAACTGACATTT_TGCGCCAGCAGCCAAGGTGGACAGGGCGGAAGGGAGCTGTTTTTT;TGTGCCAGTAGCTACGCGGTGGGGAGGCAGCCCCAGCATTTT
## 8 NA_TGCGCCAGCAGCTTGAGGGAAACCAACTATGGCTACACCTTC
## 9 TGTGCTGTGCAGGCCAAGCGGTATACTGGAGGCTTCAAAACTATCTTT_TGCGCCAGCAGCTTGGGAACGGGGACAGGGGTTGAAGCTTTCTTT;TGTGCCATCGATCCGGGACTACTCACCGGGGAGCTGTTTTTT
## 12 TGTGCTGTGGGTGGTGACACAGGCTTTCAGAAACTTGTATTT_TGTGCCAGCAGAAACTCCCAAGCCACTGAAGCTTTCTTT
## CTaa
## 1 CIVRGGSSNTGKLIF_CASIGRSFGRDTQYF
## 3 CAVQRSNDYKLSF_CASSPPRGGFTDTQYF
## 5 CIGSSGGSNYKLTF_CASSQGGQGGRELFF;CASSYAVGRQPQHF
## 8 NA_CASSLRETNYGYTF
## 9 CAVQAKRYTGGFKTIF_CASSLGTGTGVEAFF;CAIDPGLLTGELFF
## 12 CAVGGDTGFQKLVF_CASRNSQATEAFF
## CTstrict
## 1 TRAV26-1.TRAJ37.TRAC;TGCATCGTCAGGGGCGGCTCTAGCAACACAGGCAAACTAATCTTT_TRBV6-1.None.TRBJ2-3.TRBC2;TGTGCCAGTATCGGGAGGTCCTTTGGCCGAGATACGCAGTATTTT
## 3 TRAV3.TRAJ20.TRAC;TGTGCTGTGCAACGTTCTAACGACTACAAGCTCAGCTTT_TRBV3-1.None.TRBJ2-3.TRBC2;TGTGCCAGCAGCCCCCCCCGCGGCGGATTCACAGATACGCAGTATTTT
## 5 TRAV26-1.TRAJ53.TRAC;TGCATCGGCTCAAGTGGAGGTAGCAACTATAAACTGACATTT_TRBV4-1.None.TRBJ2-2.TRBC2;TRBV19.None.TRBJ1-5.TRBC1;TGCGCCAGCAGCCAAGGTGGACAGGGCGGAAGGGAGCTGTTTTTT;TGTGCCAGTAGCTACGCGGTGGGGAGGCAGCCCCAGCATTTT
## 8 NA;NA_TRBV5-1.None.TRBJ1-2.TRBC1;TGCGCCAGCAGCTTGAGGGAAACCAACTATGGCTACACCTTC
## 9 TRAV20.TRAJ9.TRAC;TGTGCTGTGCAGGCCAAGCGGTATACTGGAGGCTTCAAAACTATCTTT_TRBV5-1.None.TRBJ1-1.TRBC1;TRBV7-9.None.TRBJ2-2.TRBC2;TGCGCCAGCAGCTTGGGAACGGGGACAGGGGTTGAAGCTTTCTTT;TGTGCCATCGATCCGGGACTACTCACCGGGGAGCTGTTTTTT
## 12 TRAV8-3.TRAJ8.TRAC;TGTGCTGTGGGTGGTGACACAGGCTTTCAGAAACTTGTATTT_TRBV12-4.None.TRBJ1-1.TRBC1;TGTGCCAGCAGAAACTCCCAAGCCACTGAAGCTTTCTTT
## Type
## 1 B
## 3 B
## 5 B
## 8 B
## 9 B
## 12 BAfter assigning the clone by barcode, we can export the paired
clonotypes using exportClones() to save for later use or to
use in other pipelines.
format
write.file
dir
directory location to save the csv
file.name
the csv file name