R/phylip.R
repClonalFamily.RdThis function uses the PHYLIP package to make phylogenetic analysis. For making trees it uses maximum parsimony methods.
repClonalFamily(.data, .vis_groups, .threads, .nofail)The data to be processed, output of repAlignLineage() function.
Groups for visualization, used to annotate specific clones on chart and display them in different colors. This is a named list, where names are for the chart legend, and list items are clone IDs that belong to the groups. It's not necessary to assign groups to all clonotypes; unassigned ones will be displayed on the chart as "Clonotype" category. It's also possible to assign multiple clonotypes to the same group by providing nested lists or vectors of clone IDs instead of single clone IDs. Example: .vis_groups = list(A = 817, B = 201, C = list(303, 42))
Number of threads to use.
Returns NA instead of stopping if PHYLIP is not installed. Used to avoid raising errors in examples on computers where PHYLIP is not installed.
Dataframe or list of dataframes (if input is a list with multiple samples). The dataframe has these columns: * Cluster: cluster name * Germline.Input: germline sequence, like it was in the input; not aligned * Germline.Output: germline sequence, parsed from PHYLIP dnapars function output; it contains difference of germline from the common ancestor; "." characters mean matching letters * Common.Ancestor: common ancestor sequence, parsed from PHYLIP dnapars function output * Trunk.Length: mean trunk length, representing the distance between the most recent common ancestor and germline sequence as a measure of the maturity of a lineage * Tree: output tree in "phylo" format, loaded from by PHYLIP dnapars function output * TreeStats: nested dataframe containing data about tree nodes, needed for visualization * Sequences: nested dataframe containing all sequences for this combination of cluster and germline; it contains regions from original sequences, saved for repSomaticHypermutation() calculation, and also data needed for visualizations
data(bcrdata)
bcr_data <- bcrdata$data
bcr_data %>%
seqCluster(seqDist(bcr_data), .fixed_threshold = 3) %>%
repGermline(.threads = 1) %>%
repAlignLineage(.min_lineage_sequences = 2, .align_threads = 2, .nofail = TRUE) %>%
repClonalFamily(.threads = 1, .nofail = TRUE)
#> Warning: Genes or alleles IGHV4-55 from sample full_clones not found in the reference and will be dropped!
#> Probably, species argument is wrong (current value: HomoSapiens) or the data contains non-BCR genes.
#> $full_clones
#> Cluster
#> 1 IGHV4-61/IGHJ4_length_45_cluster_1
#> 2 IGHV4-61/IGHJ4_length_63_cluster_1
#> 3 IGHV5-51/IGHJ4_length_60_cluster_1
#> 4 IGHV5-51/IGHJ5_length_45_cluster_1
#> Germline.Input
#> 1 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 2 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 3 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 4 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> Germline.Output
#> 1 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 2 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 3 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 4 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> Common.Ancestor
#> 1 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCCATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATGTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGTTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTCTGTGCGAGAGGCGCCGGGGACTACRSCACTCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
#> 2 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGTACCAACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCATTAGACACGTCCAAGAACCAGTTCTCCCTGAACCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTTTTGTGCGAGAGATCATCACAGTTTCTATGATACWAGTGGTTATTATCCCTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
#> 3 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGACCAGGTCACCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGTRAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAASCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
#> 4 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGDTGGGGABCATCTATCCTCGTGACTCTGATACCAGATACAGTCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATVTATTACTGTRCGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
#> Trunk.Length
#> 1 7
#> 2 8
#> 3 6
#> 4 6
#> Tree
#> 1 4, 4, 4, 1, 2, 3, 0.02747, 0.03297, 0.01923, 1, ID_643, ID_42, Germline
#> 2 4, 4, 4, 1, 2, 3, 0.0144, 0.00131, 0.02094, 1, ID_123, ID_119, Germline
#> 3 4, 4, 4, 1, 2, 3, 0.00798, 0.00266, 0.01596, 1, ID_792, ID_416, Germline
#> 4 4, 4, 4, 1, 2, 3, 0.03186, 0.04017, 0.01385, 1, ID_987, ID_283, Germline
#> TreeStats
#> 1 CommonAncestor_1, ID_643, ID_42, Germline, CommonAncestor, Clonotype, Clonotype, Germline, 1, 301, 26, 1, Germline, CommonAncestor_1, CommonAncestor_1, NA, 7, 9, 11, 0, 7, 5, 8, 0, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCCATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATGTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGTTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTCTGTGCGAGAGGCGCCGGGGACTACRSCACTCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGATATATTCATTACAGTGGGAACTCCTTCTACAACCCCTCCCTCAAAAGTCGAGTCACCATGTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAGGTTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTCTGTGCGAGAGGCGCCGGGGACTACGCCACTCCCTTTGACTACTGGGGCCCGGGAACCCTGGTCACCGTCTCCTCAG, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATGTCCATCACAGTGGGAGCACCAATTACAATCCCTCCCTCAAGCGTCGAGTCACCATGTCAGTAGACACGGCCAGGAAGCAGTTGTCCCTGAAATTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTCTGTGCGAGAGGCGCCGGGGACTACAGCACTCCCTTTGACTACTGGGGCCAGGGAGCCCTGGTCACCGTCTCCTCAG, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 2 CommonAncestor_1, ID_123, ID_119, Germline, CommonAncestor, Clonotype, Clonotype, Germline, 1, 53, 290, 1, Germline, CommonAncestor_1, CommonAncestor_1, NA, 8, 5, 0, 0, 7, 4, 0, 0, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGTACCAACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCATTAGACACGTCCAAGAACCAGTTCTCCCTGAACCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTTTTGTGCGAGAGATCATCACAGTTTCTATGATACWAGTGGTTATTATCCCTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGAATATCTATTACAGTGGGACTACCAACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCCTTAGACACGTCCAAGAACCAGTTCTCCCTGACCCTGAGGTCTGTGACCGCTGCGGACACGGCCGTGTATTTTTGTGCGAGAGATCATCACAGTTTCTATGATACAAGTGGTTATTATCCCTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGTACCAACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCATTAGACACGTCCAAGAACCAGTTCTCCCTGAACCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTTTTGTGCGAGAGATCATCACAGTTTCTATGATACTAGTGGTTATTATCCCTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 3 CommonAncestor_1, ID_792, ID_416, Germline, CommonAncestor, Clonotype, Clonotype, Germline, 1, 777, 21, 1, Germline, CommonAncestor_1, CommonAncestor_1, NA, 6, 2, 0, 0, 7, 1, 0, 0, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGACCAGGTCACCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGTRAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAASCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGAATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGACCAGGTCAGCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGTAAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAACCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGACCAGGTCACCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGTGAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAAGCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> 4 CommonAncestor_1, ID_987, ID_283, Germline, CommonAncestor, Clonotype, Clonotype, Germline, 1, 57, 184, 1, Germline, CommonAncestor_1, CommonAncestor_1, NA, 6, 12, 15, 0, 6, 6, 9, 0, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGDTGGGGABCATCTATCCTCGTGACTCTGATACCAGATACAGTCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATVTATTACTGTRCGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGTTGGGGAGCATCTACCCTCGTGACTCTGACACTAGATACAGTCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCCTCAGTACCGCCTACTTGCAGTGGAACAGCCTGCAGGCCTCGGACACCGCCATCTACTACTGTGCGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGAAAAGGCCTGGAGTGGGTGGGATCGATCTATCCTCGTGACTCTGATATCAGATACAATCCGTCCTTCCAAGGCCAAGTCACCATCTCAGCCGACAGGTCCACCACCACCGCCTACCTGCAGTGGAGCAGTCTGAAGGCCTCGGACACCGCCATATATTACTGTACGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGGGGCCAGGGAGCCCTGGTCACCGTCTCCTCAG, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCCAAGGAACCCTGGTCACCGTCTCCTCAG
#> Sequences
#> 1 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATGTCCATCACAGTGGGAGCACCAATTACAATCCCTCCCTCAAGCGTCGAGTCACCATGTCAGTAGACACGGCCAGGAAGCAGTTGTCCCTGAAATTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTCTGTGCGAGAGGCGCCGGGGACTACAGCACTCCCTTTGACTACTGGGGCCAGGGAGCCCTGGTCACCGTCTCCTCAG, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGATATATTCATTACAGTGGGAACTCCTTCTACAACCCCTCCCTCAAAAGTCGAGTCACCATGTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAGGTTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTCTGTGCGAGAGGCGCCGGGGACTACGCCACTCCCTTTGACTACTGGGGCCCGGGAACCCTGGTCACCGTCTCCTCAG, 42, 643, 26, 301, IGHV4-61*01, IGHV4-61*01, IGHJ4*01, IGHJ4*01, ggtggctccgtcagcagtggtggttactac, ggtggctccgtcagcagtggtggttactac, GTCCATCACAGTGGGAGCACC, ATTCATTACAGTGGGAACTCC, TGTGCGAGAGGCGCCGGGGACTACAGCACTCCCTTTGACTACTGG, TGTGCGAGAGGCGCCGGGGACTACGCCACTCCCTTTGACTACTGG, caggtgcagctgcaggagtcgggcccaggactggtgaagccttcggagaccctgtccctcacctgcactgtctct, caggtgcagctgcaggagtcgggcccaggactggtgaagccttcggagaccctgtccctcacctgcactgtctct, tggagctggatccggcagCCCCCAGGGAAGGGACTGGAGTGGATTGGGTAT, tggagctggatccggcagCCCCCAGGGAAGGGACTGGAGTGGATTGGATAT, AATTACAATCCCTCCCTCAAGCGTCGAGTCACCATGTCAGTAGACACGGCCAGGAAGCAGTTGTCCCTGAAATTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTC, TTCTACAACCCCTCCCTCAAAAGTCGAGTCACCATGTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAGGTTGACCTCTGTGACCGCTGCGGACACGGCCGTGTATTTC, GGCCAGGGAGCCCTGGTCACCGTCTCCTCAG, GGCCCGGGAACCCTGGTCACCGTCTCCTCAG, QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGGYYWSWIRQPPGKGLEWIGYVHHSGSTNYNPSLKRRVTMSVDTARKQLSLKLTSVTAADTAVYF, QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGGYYWSWIRQPPGKGLEWIGYIHYSGNSFYNPSLKSRVTMSVDTSKNQFSLRLTSVTAADTAVYF, GQGALV~SPSPQ, GPGTLV~SPSPQ
#> 2 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGTACCAACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCATTAGACACGTCCAAGAACCAGTTCTCCCTGAACCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTTTTGTGCGAGAGATCATCACAGTTTCTATGATACTAGTGGTTATTATCCCTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGAATATCTATTACAGTGGGACTACCAACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCCTTAGACACGTCCAAGAACCAGTTCTCCCTGACCCTGAGGTCTGTGACCGCTGCGGACACGGCCGTGTATTTTTGTGCGAGAGATCATCACAGTTTCTATGATACAAGTGGTTATTATCCCTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, 119, 123, 290, 53, IGHV4-61*01, IGHV4-61*01, IGHJ4*01, IGHJ4*01, ggtggctccgtcagcagtggtggttactac, ggtggctccgtcagcagtggtggttactac, ATCTATTACAGTGGGAGTACC, ATCTATTACAGTGGGACTACC, TGTGCGAGAGATCATCACAGTTTCTATGATACTAGTGGTTATTATCCCTACTTTGACTACTGG, TGTGCGAGAGATCATCACAGTTTCTATGATACAAGTGGTTATTATCCCTACTTTGACTACTGG, caggtgcagctgcaggagtcgggcccaggactggtgaagccttcggagaccctgtccctcacctgcactgtctct, caggtgcagctgcaggagtcgggcccaggactggtgaagccttcggagaccctgtccctcacctgcactgtctct, tggagctggatccggcagcccccagggaagggactgGAGTGGATTGGGTAT, tggagctggatccggcagcccccagggaagggactgGAGTGGATTGGGAAT, AACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCATTAGACACGTCCAAGAACCAGTTCTCCCTGAACCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTTT, AACTACAACCCCTCCCTCAAGAGTCGAGTCAGCATATCCTTAGACACGTCCAAGAACCAGTTCTCCCTGACCCTGAGGTCTGTGACCGCTGCGGACACGGCCGTGTATTTT, GGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GGCCAGGGAACCCTGGTCACCGTCTCCTCAG, QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGGYYWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVSISLDTSKNQFSLNLSSVTAADTAVYF, QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGGYYWSWIRQPPGKGLEWIGNIYYSGTTNYNPSLKSRVSISLDTSKNQFSLTLRSVTAADTAVYF, GQGTLV~SPSPQ, GQGTLV~SPSPQ
#> 3 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGACCAGGTCACCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGTGAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAAGCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGAATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGACCAGGTCAGCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGTAAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAACCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, 416, 792, 21, 777, IGHV5-51*01, IGHV5-51*01, IGHJ4*01, IGHJ4*01, ggatacagctttaccagctactgg, ggatacagctttaccagctactgg, ATCTATCCTGGTGACTCTGATACC, ATCTATCCTGGTGACTCTGATACC, TGTGTGAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAAGCTTTGACTACTGG, TGTGTAAGACACTCTGGTAAGATAGAATCATCTGTGGGCCCCAGAACCTTTGACTACTGG, gaggtgcagctggtgcagtctggagcagaggtgaaaaagcccggggagtctctgaagatctcctgtaagggttct, gaggtgcagctggtgcagtctggagcagaggtgaaaaagcccggggagtctctgaagatctcctgtaagggttct, atcggctgggtgcgccagatgcccgggaaaggcctgGAGTGGATGGGGATC, atcggctgggtgcgccagatgcccgggaaaggcctgGAGTGGATGGGAATC, AGATACAGCCCGTCCTTCCAAGACCAGGTCACCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTAC, AGATACAGCCCGTCCTTCCAAGACCAGGTCAGCATGTCAGTCGGCAAGTCCATCGGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTAC, GGCCAGGGAACCCTGGTCACCGTCTCCTCAG, GGCCAGGGAACCCTGGTCACCGTCTCCTCAG, EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQDQVTMSVGKSIGTAYLQWSSLKASDTAMYY, EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQDQVSMSVGKSIGTAYLQWSSLKASDTAMYY, GQGTLV~SPSPQ, GQGTLV~SPSPQ
#> 4 GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGAAAAGGCCTGGAGTGGGTGGGATCGATCTATCCTCGTGACTCTGATATCAGATACAATCCGTCCTTCCAAGGCCAAGTCACCATCTCAGCCGACAGGTCCACCACCACCGCCTACCTGCAGTGGAGCAGTCTGAAGGCCTCGGACACCGCCATATATTACTGTACGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGGGGCCAGGGAGCCCTGGTCACCGTCTCCTCAG, GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGTTGGGGAGCATCTACCCTCGTGACTCTGACACTAGATACAGTCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCCTCAGTACCGCCTACTTGCAGTGGAACAGCCTGCAGGCCTCGGACACCGCCATCTACTACTGTGCGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG, 283, 987, 184, 57, IGHV5-51*01, IGHV5-51*01, IGHJ5*01, IGHJ5*01, ggatacagctttaccagctactgg, ggatacagctttaccagctactgg, ATCTATCCTCGTGACTCTGATATC, ATCTACCCTCGTGACTCTGACACT, TGTACGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGG, TGTGCGAGACAACACCCTTTAGATAGTCGTGTCTGGTACACTTGG, gaggtgcagctggtgcagtctggagcagaggtgaaaaagcccggggagtctctgaagatctcctgtaagggttct, gaggtgcagctggtgcagtctggagcagaggtgaaaaagcccggggagtctctgaagatctcctgtaagggttct, atcggctgggtgcgccagatgCCCGGAAAAGGCCTGGAGTGGGTGGGATCG, atcggctgggtgcgccagatgCCCGGGAAAGGCCTGGAGTGGTTGGGGAGC, AGATACAATCCGTCCTTCCAAGGCCAAGTCACCATCTCAGCCGACAGGTCCACCACCACCGCCTACCTGCAGTGGAGCAGTCTGAAGGCCTCGGACACCGCCATATATTAC, AGATACAGTCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCCTCAGTACCGCCTACTTGCAGTGGAACAGCCTGCAGGCCTCGGACACCGCCATCTACTAC, GGCCAGGGAGCCCTGGTCACCGTCTCCTCAG, GGCCAGGGAACCCTGGTCACCGTCTCCTCAG, EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWVGSIYPRDSDIRYNPSFQGQVTISADRSTTTAYLQWSSLKASDTAIYY, EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWLGSIYPRDSDTRYSPSFQGQVTISADKSLSTAYLQWNSLQASDTAIYY, GQGALV~SPSPQ, GQGTLV~SPSPQ
#>
#> attr(,"class")
#> [1] "clonal_family" "list"