new_scGPS_object generates a scGPS object in the
SingleCellExperiment class for use with the scGPS package. This
object contains an expression matrix, associated metadata (cells, genes,
clusters). The data are expected to be normalised counts.
new_scGPS_object( ExpressionMatrix = NULL, GeneMetadata = NULL, CellMetadata = NULL, LogMatrix = NULL )
| ExpressionMatrix | An expression matrix in data.frame or matrix format. Rows should represent a transcript and its normalised counts, while columns should represent individual cells. |
|---|---|
| GeneMetadata | A data frame or vector containing gene identifiers used in the expression matrix. The first column should hold the gene identifiers you are using in the expression matrix. Other columns contain information about the genes, such as their corresponding ENSEMBL transcript identifiers. |
| CellMetadata | A data frame containing cell identifiers (usually barcodes) and an integer representing which batch they belong to. The column containing clustering information needs to be the first column in the CellMetadata dataframe If clustering information is not available, users can run CORE function and add the information to the scGPS before running scGPS prediction |
| LogMatrix | optional input for a log matrix of the data. If no log matrix is supplied one will be created for the object |
This function generates an scGPS object belonging to the SingleCellExperiment.
SingleCellExperiment
Quan Nguyen, 2018-04-06
day2 <- day_2_cardio_cell_sample t <-new_scGPS_object(ExpressionMatrix = day2$dat2_counts, GeneMetadata = day2$dat2geneInfo, CellMetadata = day2$dat2_clusters) colData(t); show(t); colnames(t)#> DataFrame with 590 rows and 1 column #> X #> <integer> #> 2_CCCATGTGTCTCAT-1 2 #> 1_TACGGCCTAGAACA-1 1 #> 2_ACGATCGAGTACGT-1 3 #> 2_TACGGCCTAAAGTG-1 2 #> 2_AACTCTTGGGTATC-1 2 #> ... ... #> 1_TTCAGACTTCGTGA-1 1 #> 2_CGCAAATGCGTTGA-1 1 #> 1_CAAGTCGATTCTAC-1 1 #> 2_AAGATTACGAGCAG-1 1 #> 2_TATCTTCTCGCCTT-1 1#> class: SingleCellExperiment #> dim: 5000 590 #> metadata(0): #> assays(2): counts logcounts #> rownames(5000): TMEM182 RP11-424G14.1 ... TTPAL SUFU #> rowData names(2): GeneSymbol EnsemblID #> colnames(590): 2_CCCATGTGTCTCAT-1 1_TACGGCCTAGAACA-1 ... #> 2_AAGATTACGAGCAG-1 2_TATCTTCTCGCCTT-1 #> colData names(1): X #> reducedDimNames(0): #> spikeNames(0): #> altExpNames(0):#> [1] "2_CCCATGTGTCTCAT-1" "1_TACGGCCTAGAACA-1" "2_ACGATCGAGTACGT-1" #> [4] "2_TACGGCCTAAAGTG-1" "2_AACTCTTGGGTATC-1" "2_GAAAGATGTTTGGG-1" #> [7] "2_TCATCATGAGTCTG-1" "2_GACACTGAGGAGGT-1" "2_GCGATATGTACTGG-1" #> [10] "1_GATATTGAGCCCTT-1" "2_GGACGCACTGACTG-1" "2_TAGGCATGTCTATC-1" #> [13] "2_GCAGATACTCCAGA-1" "1_TAAGATACATCTTC-1" "1_TACTTTCTACCATG-1" #> [16] "1_CAAGAAGATTTCTG-1" "2_ATCGAGTGTGCACA-1" "2_CATACTACGGTATC-1" #> [19] "2_CCTCATCTAAAACG-1" "2_GGACGCTGACACAC-1" "1_ATTACCACAAGGTA-1" #> [22] "2_ATTTCCGAACCTCC-1" "1_CCTCTACTCTACCC-1" "2_AGAAGATGCTCCCA-1" #> [25] "2_CTATAGCTCTCAGA-1" "2_AAGTTCCTGTAAGA-1" "2_GGCACGTGCGTACA-1" #> [28] "2_GCGAGAGACTAGCA-1" "2_TTCACAACTTCCAT-1" "2_ATCCTAACGCTGAT-1" #> [31] "1_ACGGAACTGCTACA-1" "2_TGCAATCTCTGCTC-1" "1_CGACTCACTGACAC-1" #> [34] "2_CCGAAAACGACACT-1" "2_CAGACCCTCTTCGC-1" "2_CCCAGACTCCAGTA-1" #> [37] "2_GCGACTCTGCATCA-1" "2_GAACACACGAAACA-1" "2_GTCCCATGTCCTGC-1" #> [40] "2_AACTCACTGGAGCA-1" "2_ATCTTGACGGTTAC-1" "2_AAAGACGAGTTAGC-1" #> [43] "2_CACATGGATTTGTC-1" "1_CCGACTACTCCTTA-1" "2_TTACACACCCCGTT-1" #> [46] "2_CCATCCGAAAGGCG-1" "2_TTCTACGATGAAGA-1" "2_GCATGATGAGTGCT-1" #> [49] "2_CGCTACACGGTCAT-1" "2_TTCAACACAGCAAA-1" "2_GTAGACTGCTTGAG-1" #> [52] "2_TTCATCGAGGGTGA-1" "1_CGAAGACTACTGTG-1" "2_AGAGCTACGGACGA-1" #> [55] "2_GCTATACTGTTGTG-1" "2_AGAGTGCTTGCTAG-1" "1_AGAATACTCTGATG-1" #> [58] "2_CTACGCACGGAAAT-1" "2_GATATCCTTCGCTC-1" "2_ATTAGATGCCACAA-1" #> [61] "1_CGAGTATGGAGACG-1" "1_GCGGACTGCTTGGA-1" "2_ACTCCCGACCACAA-1" #> [64] "2_GAGCAGGAAGAATG-1" "2_AGGGAGTGGTAAGA-1" "2_TAATGAACAAGGGC-1" #> [67] "2_GCACGGACCTCATT-1" "2_TCCGGACTAGAATG-1" "1_AAAGACGACACTGA-1" #> [70] "2_AGAAAGTGCATTTC-1" "1_CACATACTCGGTAT-1" "1_AACGGTTGCGCAAT-1" #> [73] "2_ATCCATACTGTGCA-1" "2_ATGAGAGATATGCG-1" "2_GTGTCAGATATGCG-1" #> [76] "2_AAGCCTGAGCTATG-1" "1_AACTCTTGTGACAC-1" "1_AACCCAGAGCATAC-1" #> [79] "2_GTTGACGATCTAGG-1" "1_TAGATTGAGTATCG-1" "1_CCCAGTTGCGTTGA-1" #> [82] "2_GTTAGGTGCCAAGT-1" "2_TTCCTAGACGAATC-1" "2_AAGCACTGGGTGAG-1" #> [85] "2_AATCCTTGGCGTAT-1" "2_TACCGCTGTCAGAC-1" "2_TGGAACTGGAGCTT-1" #> [88] "1_GAACCAACCTGAGT-1" "2_CGACTCTGCTGTCC-1" "1_CATCATACAGGTCT-1" #> [91] "2_ACCCTCGACCTATT-1" "2_TGGATTCTGTAAGA-1" "2_ACATGGTGCAGAGG-1" #> [94] "1_TCGATTTGTTGGTG-1" "2_CCCGGAGACAAGCT-1" "2_CTTATCGACCTATT-1" #> [97] "1_GTTCAGGACTTACT-1" "2_CGACCTACCCAATG-1" "1_CAAGGACTCTAGCA-1" #> [100] "2_CGACCGGAGTACAC-1" "2_GGGCACACGCGTTA-1" "1_GTCCAAGATTTCGT-1" #> [103] "2_CAAGCTGAATCGGT-1" "2_GGAACACTCTACTT-1" "1_CCAGTGCTACCTTT-1" #> [106] "2_TCATTCGAGTCACA-1" "2_GATTCGGACGAATC-1" "1_ACGGAACTCTTCTA-1" #> [109] "2_ACCCGTACGGTTCA-1" "2_CATAAAACGTTCAG-1" "2_GCCTACACTTTCAC-1" #> [112] "2_TGGTAGTGGAGATA-1" "1_CTTACTGAGTCTAG-1" "1_AAGATTACCAGTTG-1" #> [115] "2_ATATGAACGTATCG-1" "1_GCACAATGATCGGT-1" "2_GGGAACGATTCCGC-1" #> [118] "1_GCGAGAGAATTCCT-1" "1_TACTACTGAGGTTC-1" "2_ATTGATGACCACAA-1" #> [121] "1_CCAGTCTGCTCGAA-1" "2_TTTCTACTACCAAC-1" "2_AGAAACGAGAAACA-1" #> [124] "2_ATTTCTCTTCTACT-1" "2_GTGTGATGCATGAC-1" "2_ACTGCCACTTCTTG-1" #> [127] "2_TAGAGCACGCATCA-1" "2_TATCAGCTTTGTCT-1" "1_ATGTCGGAGTTAGC-1" #> [130] "2_ACAATTGATGCTCC-1" "1_AGTAATACGTACCA-1" "1_ACTGAGACTTCTTG-1" #> [133] "2_AAATCTGATACAGC-1" "2_GTTGAGTGTTAGGC-1" "2_GCACAAACAAGCCT-1" #> [136] "2_TACGAGTGTGAAGA-1" "2_CAGGAACTACCCTC-1" "1_CTCGAGCTGACAAA-1" #> [139] "2_TGCCCAACCTGAGT-1" "2_AGTACGTGAAGGGC-1" "2_CACTATACCTGACA-1" #> [142] "2_ATCGCCACATTGGC-1" "2_TTCAGACTAAAGCA-1" "2_CACTGAGAACGGGA-1" #> [145] "2_ACTACTACGATACC-1" "2_TGGAGGGACTACTT-1" "2_TGCAGATGATCGTG-1" #> [148] "2_TTAGACCTTGGAAA-1" "1_AGTAAGGACCACCT-1" "1_GATTCGGAGGAAAT-1" #> [151] "1_AGGTACACGTTTGG-1" "2_TAAGTAACGCGAGA-1" "2_TTCAAAGATCGACA-1" #> [154] "2_AAGCACTGTCGTGA-1" "2_CCAAGAACACACTG-1" "2_CGTGCACTAGAGGC-1" #> [157] "2_TATACGCTTCAGGT-1" "2_ATGCGATGGGTTTG-1" "2_GTTAGGTGAACGGG-1" #> [160] "2_CGGTCACTACTCAG-1" "2_CAGCTCACTTCATC-1" "2_GTATCACTCATTGG-1" #> [163] "2_TTGCTAACCTAGAC-1" "1_TGCTGAGATGCTCC-1" "1_GTTAGGTGGTTGAC-1" #> [166] "2_TACTCAACGTAAAG-1" "2_GATCCCTGCTATTC-1" "2_ACAACCGACGGAGA-1" #> [169] "2_TCAGACGAGTTTCT-1" "2_CGACGTCTCGTCTC-1" "2_GACCAAACTGCTTT-1" #> [172] "2_CTGAAGACACAGCT-1" "2_TGGACCCTCCAATG-1" "1_TACTTTCTGAGAGC-1" #> [175] "1_GTCGCACTCGAGTT-1" "2_CCCAACTGGGATTC-1" "2_AGGTGGGATTGGCA-1" #> [178] "2_GACTACGAGAACTC-1" "2_CTAGTTACGTATGC-1" "1_GGCCGAACTTCTCA-1" #> [181] "2_TAACGTCTGAGAGC-1" "2_TAGTCGGATTGAGC-1" "1_CACTATACTCGCCT-1" #> [184] "1_GACCATGACCGCTT-1" "2_TGACTTACGAACTC-1" "1_ATCTACTGCTGTTT-1" #> [187] "1_GATCGATGTACGCA-1" "2_TTCAACACATGTGC-1" "2_CATTGACTACGGAG-1" #> [190] "2_TTACGACTCGAACT-1" "2_AATCGGTGGGATTC-1" "2_TTGACACTCTAGCA-1" #> [193] "2_TGACCAGATTCTAC-1" "2_TAACCGGACTTCCG-1" "2_TCGCACACTGACTG-1" #> [196] "1_GTTAACCTTGAGGG-1" "2_TGATTAGAGGTATC-1" "1_CAGCCTACATGGTC-1" #> [199] "2_ATTGGTCTCTCCCA-1" "2_TACTAAGACACTTT-1" "2_TAAACAACCGCAAT-1" #> [202] "2_TTTAGCTGTCTGGA-1" "1_TGTAGGTGACACAC-1" "2_TTCAGTACACCCTC-1" #> [205] "2_CGACAAACAGCAAA-1" "2_GAACACACAGCCTA-1" "2_CGCTACTGCGCTAA-1" #> [208] "2_CAAATTGAACTGGT-1" "2_AAGGCTACGCTAAC-1" "2_AGCAAAGACTTGAG-1" #> [211] "2_AACCTACTCACTCC-1" "2_GAGTACACCATGGT-1" "2_CGGACTCTTTTGGG-1" #> [214] "2_CTATACTGTGGAAA-1" "2_ACCACGCTAACAGA-1" "2_ATTCCATGAGGTTC-1" #> [217] "2_CGGACTCTTCGTAG-1" "2_CGACCTTGACCAAC-1" "2_TTGCTATGCCTCGT-1" #> [220] "2_GTATCTACATGGTC-1" "1_TCCCTACTCATTGG-1" "2_ACGTAGACAGCAAA-1" #> [223] "2_GATTCTTGAGGGTG-1" "2_AAGAGATGTAACGC-1" "2_GCTCCATGTCCTCG-1" #> [226] "1_GAGCTCCTGTAAGA-1" "2_AGAGCGGAAGCTAC-1" "2_CTACGGCTGCTTCC-1" #> [229] "1_AACGCCCTGCTATG-1" "2_CTGACAGAACCTAG-1" "2_ATAAACACTGGATC-1" #> [232] "2_ATACCTACTTTGCT-1" "2_GTCACAGATTTGTC-1" "1_AAGCACTGTGCAAC-1" #> [235] "2_GAGGTGGAGAGAGC-1" "2_GGGCACACTGTGCA-1" "1_AGCATCGAATTCCT-1" #> [238] "2_GGTAAAGAGTAGGG-1" "2_ATCTTTCTAGGTCT-1" "2_TCAGCAGATCTCGC-1" #> [241] "1_CCTAAGGAAGGTCT-1" "2_TGATATGATAGCGT-1" "2_AGAGGTCTAGAGAT-1" #> [244] "1_TTATGCACTAGAAG-1" "2_TACGCAGAGTATCG-1" "2_CCTCTACTACAGTC-1" #> [247] "2_TACTAAGACACCAA-1" "2_TCAATCACCTGACA-1" "2_AATGAGGATTGGTG-1" #> [250] "2_ACGAGGGAACCGAT-1" "2_ACTGTGGACATCAG-1" "2_CGACCACTCAGATC-1" #> [253] "2_ACCTCCGAATTCGG-1" "1_AAGGTCTGTCACGA-1" "1_ATTGCACTCCAGTA-1" #> [256] "2_CATAACCTTCAGTG-1" "2_GTTGAGTGTGAGAA-1" "2_CCAAGAACGCTAAC-1" #> [259] "2_AGAGAAACTCAGGT-1" "2_AAGAAGACAAACGA-1" "1_CCAGGTCTGTATGC-1" #> [262] "1_AGACACACTTTGTC-1" "2_AGTTAAACAACCTG-1" "2_TTCATGACTGCTAG-1" #> [265] "2_GATCTTTGTCCGTC-1" "2_TAATGAACCCATGA-1" "1_TATCCAACGGTCAT-1" #> [268] "2_GGAGAGACAGTAGA-1" "2_GCAACCCTCTATTC-1" "2_TCACGAGATGGTGT-1" #> [271] "2_AGGTTGTGATCGAC-1" "2_AGGCAACTGCGTAT-1" "2_CAATTCACGGTATC-1" #> [274] "2_AAATCTGACTATGG-1" "2_ACGATTCTTCCAGA-1" "2_CAAATATGAACCGT-1" #> [277] "2_GAACAGCTTTTGGG-1" "2_AACGCATGGACAGG-1" "2_GCTAGAACGGTCAT-1" #> [280] "1_GGAATCTGCACAAC-1" "2_AGCCTCTGGTCTTT-1" "1_TAGAGCACGTCAAC-1" #> [283] "2_ACAGACACGACAGG-1" "2_GGCGCATGCTGATG-1" "2_CAGCTCACACCCTC-1" #> [286] "2_ACACGAACAAGAAC-1" "2_AGCTCGCTGGCGAA-1" "2_CGGCACGAGGTGGA-1" #> [289] "2_GCAGATACAACAGA-1" "2_CAATCGGAATGTGC-1" "2_GCCAACCTTGTGCA-1" #> [292] "2_GAAGTCACCTTAGG-1" "2_CCCGGAGATGATGC-1" "1_TTTCACGAAAAGTG-1" #> [295] "1_GTGAACACCGTAGT-1" "1_GGAGGCCTTACTGG-1" "2_CTCGCATGCTCGAA-1" #> [298] "2_AGGAACCTTTCGGA-1" "2_CTCGACACCTCTTA-1" "2_ATAATCGACTTCTA-1" #> [301] "1_TAGAGCACGGACTT-1" "1_TAGCTACTTGGTTG-1" "2_GGCGGACTACTGTG-1" #> [304] "1_ACGCACCTGCTTCC-1" "2_TAAGTAACGCCTTC-1" "1_GTCCACTGACTCAG-1" #> [307] "2_TCACTATGTTCCGC-1" "2_AAAGGCCTTTCTTG-1" "2_TACGCCACGGGATG-1" #> [310] "2_TAATGCCTCCTTGC-1" "2_GAGTGTTGCATTGG-1" "2_CATCAACTCTAGAC-1" #> [313] "2_TACTCTGAGTAGCT-1" "2_AAGGTGCTTTGCGA-1" "2_TTCTCAGAGGTCAT-1" #> [316] "1_AACGTCGAGAGAGC-1" "2_GGTAGTACACCTGA-1" "1_AGGGTTTGGCCAAT-1" #> [319] "2_ACCTCCGATTGCTT-1" "2_ATTCGACTCGACTA-1" "2_CATAGTCTTGCAGT-1" #> [322] "1_TAACCGGACATGAC-1" "2_GTGATTCTACTTTC-1" "2_ATATACGAAAGTGA-1" #> [325] "1_CCAAGTGATTGCGA-1" "2_TTTGCATGGCCTTC-1" "2_GATATATGAGTCAC-1" #> [328] "1_ACGCACCTAGGAGC-1" "2_AATACTGAACTGTG-1" "2_AGTTTCACAAACAG-1" #> [331] "1_GCACACCTCATTCT-1" "2_GAGTCTGATTCAGG-1" "2_CCGCTATGCTGTGA-1" #> [334] "2_AGCAAGCTGTTGCA-1" "2_TACTGGGATAGAGA-1" "1_GGCCAGACTAGAAG-1" #> [337] "2_TAAAGTTGGAACCT-1" "2_AAGTTCCTTGAGGG-1" "2_AACTCTTGTTTCAC-1" #> [340] "2_ATCAAATGACCTCC-1" "2_GGAGCCACTTCGTT-1" "2_ACCCAAGAACGTTG-1" #> [343] "2_GTAACGTGAGAACA-1" "2_AGGGACGATTCTGT-1" "2_GAGCAGGACCACAA-1" #> [346] "2_ACAGGTACTTCGGA-1" "2_ACTGTTACGGTTCA-1" "1_CTCCACGACGCTAA-1" #> [349] "2_CTAACGGAGCAGAG-1" "2_CAATAATGTCGCAA-1" "2_AGAAGATGGGTTAC-1" #> [352] "1_CCAGATGATGCATG-1" "2_GGGAAGACAGGTTC-1" "2_TCGCCATGTCGTTT-1" #> [355] "1_CAGACAACCTCCCA-1" "2_TCTCAAACTGCCCT-1" "1_CATACTTGACCCTC-1" #> [358] "2_GGAAGGTGACTGTG-1" "1_ATGCACGAAGAGAT-1" "2_AGACTGACTGTGAC-1" #> [361] "2_AGTTTAGAGTCGTA-1" "2_CGAGAACTCTGACA-1" "2_CCGGTACTGGTTCA-1" #> [364] "2_GCTCGACTCCTCCA-1" "1_TCGGTAGAGTTCAG-1" "1_CACTCCGACTCTTA-1" #> [367] "2_CCATCCGATCTAGG-1" "2_GAAGCGGAAGCGTT-1" "2_ATCTCAACGTACCA-1" #> [370] "2_ACGACAACCCATGA-1" "2_GAAGTCTGTGCACA-1" "2_GCCACGGACCTATT-1" #> [373] "2_CCATTAACAAAACG-1" "2_AAGTTATGATGTGC-1" "2_CCACGGGATCCTCG-1" #> [376] "1_AGCATCGATGGTCA-1" "2_GCCTGACTACGGGA-1" "2_CTTTACGAATGGTC-1" #> [379] "2_AGAACGCTAGTTCG-1" "2_TAGAATACTGTCAG-1" "2_TGGACCCTCACCAA-1" #> [382] "2_ACCATTACAGAGTA-1" "1_CTCCATCTCTACGA-1" "2_AACCTTACGCTAAC-1" #> [385] "1_GAGGTGGATGCTAG-1" "2_AGAGATGATCAGGT-1" "1_TGCCGACTGGTAAA-1" #> [388] "2_CAGAAGCTCCTTTA-1" "1_ATTGCTACGTCTTT-1" "1_AACTCACTTGGGAG-1" #> [391] "2_GCACCACTCTCTAT-1" "2_TTGCATTGTCCTTA-1" "2_GAAAGATGAGAGGC-1" #> [394] "2_ACACAGACTCAGAC-1" "2_AGTTCTACATCGAC-1" "2_ATGAAACTCTCATT-1" #> [397] "1_GCAACTGAGCTGAT-1" "2_ACCTCGTGTCGTGA-1" "2_GTGGAGGAAGGTTC-1" #> [400] "1_GCCCAGGAAGCGTT-1" "1_ATCATGCTAGCAAA-1" "2_ACTTGTACTACTTC-1" #> [403] "2_TCACCTCTTTGTGG-1" "2_ATATAGTGCAACCA-1" "2_TTAGAATGGTAGGG-1" #> [406] "2_GGAGAGACATTGGC-1" "2_TTGCTAACCGTACA-1" "2_CACATACTGGTCTA-1" #> [409] "2_AATACTGATCCTGC-1" "2_TAACTCACGTCATG-1" "2_AGTCTTACTCCTAT-1" #> [412] "2_CTGATGGAGTACGT-1" "2_TTGGTACTCATTCT-1" "2_CAATGGACTCTGGA-1" #> [415] "2_TCAGTACTATTCTC-1" "2_GCCACGGACTCCAC-1" "2_CCACTTCTTCTAGG-1" #> [418] "1_TAGTTAGACCAGTA-1" "1_TAGAGAGACCTGAA-1" "2_CTCGACACTATCTC-1" #> [421] "2_CTTACAACTTCTGT-1" "2_GGAATCTGGTTGCA-1" "1_CATAAATGAGTCAC-1" #> [424] "2_ACTTGTACAAGCAA-1" "2_AGCTGCCTTTAGGC-1" "1_GATCCGCTCTGTAG-1" #> [427] "2_ATTAAGACATTCCT-1" "1_AGCCGGTGGATACC-1" "1_GAAGTGCTAGGGTG-1" #> [430] "2_CAGACTGACGACAT-1" "1_CAGACAACGGAGGT-1" "2_AGTAGGCTCATGAC-1" #> [433] "1_ACTCAGGATCGATG-1" "1_CACTGCTGTCACGA-1" "2_CACCCATGCTTACT-1" #> [436] "2_TTCGATTGTCGCCT-1" "2_CAAACTCTCCCAAA-1" "2_TTACCATGCCCTTG-1" #> [439] "2_TCCGAAGAGTAGCT-1" "1_GGCGCATGATGCTG-1" "2_GCACGTCTTGTCAG-1" #> [442] "1_ACTGTGGATCTCCG-1" "2_TAGACGTGCGTAAC-1" "1_CGGACCGAACGACT-1" #> [445] "2_GTACTACTAGGTCT-1" "2_CATTTGTGGAAACA-1" "1_TAATGATGAGAGGC-1" #> [448] "1_GTCAACGAACGGGA-1" "2_CAATCGGAAGAATG-1" "2_CATGTTTGGAGGAC-1" #> [451] "2_GCCTACACGTCGAT-1" "2_CTTACTGAGGTTTG-1" "2_AGTACTCTTAGTCG-1" #> [454] "2_GGGTTAACCTGCTC-1" "1_GGTGGAGATGACCA-1" "1_CCTGAGCTCTGCAA-1" #> [457] "2_CGCTCATGTGCCTC-1" "2_CGAAGTACTCTGGA-1" "2_GATAATACAGATCC-1" #> [460] "2_GATATTGAGCCTTC-1" "1_ACTCTCCTTGCATG-1" "1_CGAAGTACAGCACT-1" #> [463] "2_TTATGCACGGAGGT-1" "2_TCAGAGACAGTGTC-1" "2_AGCATCGAGTTGAC-1" #> [466] "2_CGTACAGACATTGG-1" "2_TCCCGATGAGTAGA-1" "2_CAGCCTACTCAGTG-1" #> [469] "2_TAATGTGATTCCGC-1" "2_AATTGTGAACACTG-1" "2_AAGCGACTCAGTCA-1" #> [472] "2_TAAGATTGTGATGC-1" "2_GACGTATGTGAACC-1" "1_GCTCAGCTTCTGGA-1" #> [475] "2_CGCAAATGGGTCTA-1" "2_ATATGAACTTCTTG-1" "1_AAGCCTGAGAGGCA-1" #> [478] "2_ACGCAATGTTTGTC-1" "2_GGACGCTGTCGACA-1" "1_TTATGGCTGGGAGT-1" #> [481] "2_GTACCCTGATCGGT-1" "1_GATCTTACTTCTGT-1" "2_CCCTACGATAGCGT-1" #> [484] "2_TTCATGTGTAAGGA-1" "2_GCAAGACTCCTTGC-1" "2_AGCGGGCTCTGTTT-1" #> [487] "2_TGATATGATATTCC-1" "2_AAACGGCTGTTCGA-1" "2_AACTCGGATATCGG-1" #> [490] "2_AAGTAACTTCAGAC-1" "2_AATAGGGACACTGA-1" "2_ACGCGGTGCTCATT-1" #> [493] "1_CATTACACATGCTG-1" "1_AACAGAGAGCCCTT-1" "2_GCGAGAGAGAAACA-1" #> [496] "2_TCTATGTGATGGTC-1" "2_CAAGCCCTGCTATG-1" "2_ATTCCATGCCTAAG-1" #> [499] "1_TTCACAACTCTATC-1" "2_AATTCCTGATCGTG-1" "1_CCAAAGTGCATTCT-1" #> [502] "2_ACCCAAGAGCCAAT-1" "2_TTGTCATGCCCGTT-1" "2_TTGAGGTGACGCAT-1" #> [505] "2_GCTATACTCTGGTA-1" "1_CTATTGACGATAAG-1" "2_TCAGCGCTAGAGTA-1" #> [508] "2_ATGAAGGAGGAAAT-1" "2_GACTACGACAATCG-1" "2_TTAGTCACGAACCT-1" #> [511] "2_CGTTATACGTCATG-1" "2_ATGTCACTAGTACC-1" "2_TGACACGACACAAC-1" #> [514] "2_CATAAAACCTCTAT-1" "1_ATGCGATGGTCTTT-1" "2_ACCGCGGAGCCATA-1" #> [517] "2_TGAGCTGATGTGCA-1" "2_GATCGAACCCACAA-1" "1_TGGCAATGGTACAC-1" #> [520] "2_CCGAAAACGGGACA-1" "1_CCCGAACTACCTAG-1" "2_GCGAAGGAGGTACT-1" #> [523] "2_CCTTAATGCGTACA-1" "2_CTCAGCACGCTATG-1" "2_GACGCCGACTGAAC-1" #> [526] "2_CCCAACTGAGAGGC-1" "2_CGTAACGATCGTGA-1" "2_GTACTACTAGTACC-1" #> [529] "1_TTCAGTTGGGCAAG-1" "2_GAACGTTGGACGTT-1" "2_CCCTAGTGCTACCC-1" #> [532] "2_ATACAATGTGGTAC-1" "2_GAGGACGAGAATCC-1" "2_CATAACCTGGTACT-1" #> [535] "2_AAGCCATGTCATTC-1" "2_GCATGATGAAACGA-1" "2_CCATAGGATGCATG-1" #> [538] "2_ACAATTGAGCATCA-1" "2_TCGTAGGAAAACAG-1" "2_ATCATCTGTCACCC-1" #> [541] "2_AGAATGGATATGGC-1" "2_AATGGAGACTATGG-1" "2_GAAGCTACGAGACG-1" #> [544] "2_AAGTCTCTTGTTCT-1" "2_ACATTCTGGGTAGG-1" "2_ACTGTGGACTGCAA-1" #> [547] "2_GACCTCTGTGCAGT-1" "2_ACTCTATGTAACCG-1" "2_GGCACTCTACTCAG-1" #> [550] "2_ACGTCAGATCGCTC-1" "2_TGGAAAGAGTACAC-1" "1_AGATCGTGGCTGTA-1" #> [553] "1_GTACGTGACTCAGA-1" "2_GTACTACTGTCATG-1" "2_ATCTGTTGTTACCT-1" #> [556] "1_TGTACTTGCGAGAG-1" "2_TATCGACTCTCAGA-1" "2_AGGCAGGAGACTAC-1" #> [559] "2_ATCATGCTTTATCC-1" "1_AAGTTATGGTTGTG-1" "2_ATAACATGGTAGGG-1" #> [562] "1_ACACGTGATTCTAC-1" "1_CCCGAACTGGCATT-1" "2_TAGCCCTGTACTCT-1" #> [565] "2_GGAGTTACACGCTA-1" "2_CGCACTTGGAAACA-1" "2_ATGCACGAGTAAAG-1" #> [568] "2_GTTAAATGGCAGAG-1" "2_CTTCACCTCGAATC-1" "2_CTGAGAACGGGACA-1" #> [571] "2_AACGGTACGGATCT-1" "1_GCATTGGAGTGTAC-1" "2_CCCTCAGACTCTTA-1" #> [574] "2_TCAGACGACTAAGC-1" "2_TCGACCTGGTCTGA-1" "2_CATTAGCTACCTGA-1" #> [577] "1_GAGCGCTGCTCATT-1" "2_CTTGATTGCTTGTT-1" "2_ATGTTGCTCTGTCC-1" #> [580] "2_TTCAAAGACTTGTT-1" "1_GCCTGACTATGCCA-1" "1_AGCCTCACAAGTGA-1" #> [583] "2_ACAATCCTCGAATC-1" "2_TATGCGGAGCGTTA-1" "2_TGATTCTGGTTGAC-1" #> [586] "1_TTCAGACTTCGTGA-1" "2_CGCAAATGCGTTGA-1" "1_CAAGTCGATTCTAC-1" #> [589] "2_AAGATTACGAGCAG-1" "2_TATCTTCTCGCCTT-1"