Dataframe of TARSs library.
getLib(comb)
| comb | composed list returned from train() function |
|---|
Dataframe containing the significant target-associated receptor sequences.
FIELD <- "vGeneName aminoAcid jGeneName" COUNT <- "copy" P_CUTOFF <- 0.1 MIN_PUBLIC <- 2 COPY_RANGE <- "1 99" listPos <- tsvDir(system.file("extdata", "Post", package="iCAT")) listNeg <- tsvDir(system.file("extdata", "Pre", package="iCAT")) naive <- readTrn(listNeg, FIELD, COUNT, COPY_RANGE, "naive") vaccs <- readTrn(listPos, FIELD, COUNT, COPY_RANGE, "vacc") mod <- train(naive, vaccs, listNeg, listPos, FIELD, COUNT, COPY_RANGE, P_CUTOFF, MIN_PUBLIC, NULL) getLib(mod)#> Sequence Positive Present Positive Absent #> 1: TCRBV01-01 CTCSADINQDTQYF TCRBJ02-05 6 52 #> 2: TCRBV01-01 CTCSAGGGAGEQYF TCRBJ02-07 6 52 #> 3: TCRBV01-01 CTCSAGTGHTEVFF TCRBJ01-01 6 52 #> 4: TCRBV01-01 CTCSARDTYEQYF TCRBJ02-07 6 52 #> 5: TCRBV01-01 CTCSARLGGYAEQFF TCRBJ02-01 6 52 #> 6: TCRBV02-01 CASSQDGGGTGQLYF TCRBJ02-02 6 52 #> 7: TCRBV02-01 CASSQDPGGGYEQYF TCRBJ02-07 6 52 #> 8: TCRBV03-01 CASSLAPDSGNTLYF TCRBJ01-03 6 52 #> 9: TCRBV03-01 CASSLNSNSDYTF TCRBJ01-02 6 52 #> 10: TCRBV03-01 CASSLSGGYEQYF TCRBJ02-07 6 52 #> 11: TCRBV03-01 CASSPDSSAETLYF TCRBJ02-03 6 52 #> 12: TCRBV03-01 CASSPGQGDTEVFF TCRBJ01-01 6 52 #> 13: TCRBV03-01 CASSSGDSDYTF TCRBJ01-02 6 52 #> 14: TCRBV03-01 CASSWTGQDTQYF TCRBJ02-05 6 52 #> 15: TCRBV04-01 CASSLRDGQDTQYF TCRBJ02-05 6 52 #> 16: TCRBV04-01 CASSWTGSGNTLYF TCRBJ01-03 6 52 #> 17: TCRBV04-01 CASSYREDTQYF TCRBJ02-05 6 52 #> 18: TCRBV05-01 CASSPGTNNQAPLF TCRBJ01-05 6 52 #> 19: TCRBV05-01 CASSQGYQDTQYF TCRBJ02-05 6 52 #> 20: TCRBV12-01 CASSLQNTLYF TCRBJ02-04 6 52 #> 21: TCRBV12-01 CASSPDRGQNTLYF TCRBJ02-04 6 52 #> 22: TCRBV12-01 CASSPPGQLYF TCRBJ02-02 6 52 #> 23: TCRBV12-02 CASSLEAGGAETLYF TCRBJ02-03 6 52 #> 24: TCRBV13-01 CASRLRDWGYEQYF TCRBJ02-07 6 52 #> 25: TCRBV13-01 CASRRQGNSDYTF TCRBJ01-02 6 52 #> 26: TCRBV13-01 CASSDAIYEQYF TCRBJ02-07 6 52 #> 27: TCRBV13-01 CASSDGTEQYF TCRBJ02-07 6 52 #> 28: TCRBV13-01 CASSGDNSAETLYF TCRBJ02-03 6 52 #> 29: TCRBV13-02 CASGDAAGGTGQLYF TCRBJ02-02 6 52 #> 30: TCRBV13-02 CASGDWGGATGQLYF TCRBJ02-02 6 52 #> 31: TCRBV13-02 CASGETGGNTEVFF TCRBJ01-01 6 52 #> 32: TCRBV13-02 CASGGTGVYEQYF TCRBJ02-07 6 52 #> 33: TCRBV13-02 CASGPGQSNTEVFF TCRBJ01-01 6 52 #> 34: TCRBV13-02 CASGPGRISNERLFF TCRBJ01-04 6 52 #> 35: TCRBV13-02 CASGTGGSYEQYF TCRBJ02-07 6 52 #> 36: TCRBV13-03 CASSDQGSNERLFF TCRBJ01-04 6 52 #> 37: TCRBV13-03 CASSGTVNYAEQFF TCRBJ02-01 6 52 #> 38: TCRBV13-03 CASSPDSYEQYF TCRBJ02-07 6 52 #> 39: TCRBV13-03 CASSPQGAGNTLYF TCRBJ01-03 6 52 #> 40: TCRBV13-03 CASTGQANTEVFF TCRBJ01-01 6 52 #> 41: TCRBV14-01 CASSSTGRNNQAPLF TCRBJ01-05 6 52 #> 42: TCRBV15-01 CASSGDNAETLYF TCRBJ02-03 6 52 #> 43: TCRBV16-01 CASSFKDTQYF TCRBJ02-05 6 52 #> 44: TCRBV16-01 CASSPTGGGNTLYF TCRBJ01-03 6 52 #> 45: TCRBV19-01 CASSIAGTGNERLFF TCRBJ01-04 6 52 #> 46: TCRBV19-01 CASSPTTYEQYF TCRBJ02-07 6 52 #> 47: TCRBV19-01 CASSRDNNYAEQFF TCRBJ02-01 6 52 #> 48: TCRBV19-01 CASSTGGVYEQYF TCRBJ02-07 6 52 #> 49: TCRBV26-01 CASSLGLNQDTQYF TCRBJ02-05 6 52 #> 50: TCRBV26-01 CASSLRGEVFF TCRBJ01-01 6 52 #> 51: TCRBV26-01 CASSPGQTEVFF TCRBJ01-01 6 52 #> 52: TCRBV29-01 CASSFQQDTQYF TCRBJ02-05 6 52 #> 53: TCRBV29-01 CASSPTGSGNTLYF TCRBJ01-03 6 52 #> 54: TCRBV29-01 CASSTSNSDYTF TCRBJ01-02 6 52 #> 55: TCRBV31-01 CAWSRNSDYTF TCRBJ01-02 6 52 #> 56: TCRBV01-01 CTCSAAGTGVGNTLYF TCRBJ01-03 7 51 #> 57: TCRBV03-01 CASSSDRHQDTQYF TCRBJ02-05 7 51 #> 58: TCRBV04-01 CASSHRDGQDTQYF TCRBJ02-05 7 51 #> 59: TCRBV04-01 CASSLTAYEQYF TCRBJ02-07 7 51 #> 60: TCRBV05-01 CASSQDLGPYEQYF TCRBJ02-07 7 51 #> 61: TCRBV05-01 CASSQDRQGYEQYF TCRBJ02-07 7 51 #> 62: TCRBV05-01 CASSQEGINQDTQYF TCRBJ02-05 7 51 #> 63: TCRBV05-01 CASSQEGLGGREQYF TCRBJ02-07 7 51 #> 64: TCRBV05-01 CASSQEGTGTETLYF TCRBJ02-03 7 51 #> 65: TCRBV05-01 CASSQETGNTEVFF TCRBJ01-01 7 51 #> 66: TCRBV12-01 CASSLGTVSYNSPLYF TCRBJ01-06 7 51 #> 67: TCRBV12-02 CASSLTGGSSYEQYF TCRBJ02-07 7 51 #> 68: TCRBV12-02 CASSPTTSAETLYF TCRBJ02-03 7 51 #> 69: TCRBV13-02 CASGEGLGEQYF TCRBJ02-07 7 51 #> 70: TCRBV13-03 CASSDPGGNERLFF TCRBJ01-04 7 51 #> 71: TCRBV19-01 CASSIRAEQYF TCRBJ02-07 7 51 #> 72: TCRBV31-01 CAWSLAGDNQAPLF TCRBJ01-05 7 51 #> 73: TCRBV03-01 CASSLVGASAETLYF TCRBJ02-03 9 49 #> 74: TCRBV04-01 CASSPTSYEQYF TCRBJ02-07 9 49 #> 75: TCRBV20-01 CGAREGEDTQYF TCRBJ02-05 9 49 #> 76: TCRBV01-01 CTCSAGQNNQAPLF TCRBJ01-05 11 47 #> 77: TCRBV02-01 CASSQESQNTLYF TCRBJ02-04 11 47 #> 78: TCRBV13-03 CASSDLGGQDTQYF TCRBJ02-05 11 47 #> 79: TCRBV16-01 CASSLGGAREQYF TCRBJ02-07 11 47 #> 80: TCRBV26-01 CASSLSGNTGQLYF TCRBJ02-02 11 47 #> 81: TCRBV29-01 CASSLPGTNERLFF TCRBJ01-04 11 47 #> 82: TCRBV01-01 CTCSADLGTSAETLYF TCRBJ02-03 8 50 #> 83: TCRBV14-01 CASSFTGRNNQAPLF TCRBJ01-05 8 50 #> 84: TCRBV19-01 CASSRDRYAEQFF TCRBJ02-01 8 50 #> 85: TCRBV01-01 CTCSAGTKDTQYF TCRBJ02-05 10 48 #> 86: TCRBV13-02 CASGDVGQGNERLFF TCRBJ01-04 12 46 #> 87: TCRBV13-03 CASSDAGAEQFF TCRBJ02-01 9 49 #> 88: TCRBV13-01 CASSEGSQDTQYF TCRBJ02-05 13 45 #> 89: TCRBV19-01 CASSSGTANTEVFF TCRBJ01-01 13 45 #> 90: TCRBV13-01 CASSGTGGYAEQFF TCRBJ02-01 15 43 #> 91: TCRBV13-01 CASSRQGGDERLFF TCRBJ01-04 10 48 #> 92: TCRBV14-01 CASSFTGQNNQAPLF TCRBJ01-05 10 48 #> 93: TCRBV29-01 CASGNTEVFF TCRBJ01-01 10 48 #> 94: TCRBV16-01 CASSLGTGVNQAPLF TCRBJ01-05 12 46 #> 95: TCRBV01-01 CTCSAEGVSNERLFF TCRBJ01-04 11 47 #> 96: TCRBV14-01 CASSSTGYNNQAPLF TCRBJ01-05 11 47 #> 97: TCRBV03-01 CASSPRTGGSAETLYF TCRBJ02-03 14 44 #> 98: TCRBV19-01 CASSRDKQDTQYF TCRBJ02-05 13 45 #> 99: TCRBV03-01 CASSLGFYEQYF TCRBJ02-07 14 44 #> Sequence Positive Present Positive Absent #> Negative Present Negative Absent P-Value #> 1: 0 32 0.065008684 #> 2: 0 32 0.065008684 #> 3: 0 32 0.065008684 #> 4: 0 32 0.065008684 #> 5: 0 32 0.065008684 #> 6: 0 32 0.065008684 #> 7: 0 32 0.065008684 #> 8: 0 32 0.065008684 #> 9: 0 32 0.065008684 #> 10: 0 32 0.065008684 #> 11: 0 32 0.065008684 #> 12: 0 32 0.065008684 #> 13: 0 32 0.065008684 #> 14: 0 32 0.065008684 #> 15: 0 32 0.065008684 #> 16: 0 32 0.065008684 #> 17: 0 32 0.065008684 #> 18: 0 32 0.065008684 #> 19: 0 32 0.065008684 #> 20: 0 32 0.065008684 #> 21: 0 32 0.065008684 #> 22: 0 32 0.065008684 #> 23: 0 32 0.065008684 #> 24: 0 32 0.065008684 #> 25: 0 32 0.065008684 #> 26: 0 32 0.065008684 #> 27: 0 32 0.065008684 #> 28: 0 32 0.065008684 #> 29: 0 32 0.065008684 #> 30: 0 32 0.065008684 #> 31: 0 32 0.065008684 #> 32: 0 32 0.065008684 #> 33: 0 32 0.065008684 #> 34: 0 32 0.065008684 #> 35: 0 32 0.065008684 #> 36: 0 32 0.065008684 #> 37: 0 32 0.065008684 #> 38: 0 32 0.065008684 #> 39: 0 32 0.065008684 #> 40: 0 32 0.065008684 #> 41: 0 32 0.065008684 #> 42: 0 32 0.065008684 #> 43: 0 32 0.065008684 #> 44: 0 32 0.065008684 #> 45: 0 32 0.065008684 #> 46: 0 32 0.065008684 #> 47: 0 32 0.065008684 #> 48: 0 32 0.065008684 #> 49: 0 32 0.065008684 #> 50: 0 32 0.065008684 #> 51: 0 32 0.065008684 #> 52: 0 32 0.065008684 #> 53: 0 32 0.065008684 #> 54: 0 32 0.065008684 #> 55: 0 32 0.065008684 #> 56: 0 32 0.040243471 #> 57: 0 32 0.040243471 #> 58: 0 32 0.040243471 #> 59: 0 32 0.040243471 #> 60: 0 32 0.040243471 #> 61: 0 32 0.040243471 #> 62: 0 32 0.040243471 #> 63: 0 32 0.040243471 #> 64: 0 32 0.040243471 #> 65: 0 32 0.040243471 #> 66: 0 32 0.040243471 #> 67: 0 32 0.040243471 #> 68: 0 32 0.040243471 #> 69: 0 32 0.040243471 #> 70: 0 32 0.040243471 #> 71: 0 32 0.040243471 #> 72: 0 32 0.040243471 #> 73: 1 31 0.068688656 #> 74: 1 31 0.068688656 #> 75: 1 31 0.068688656 #> 76: 2 30 0.088006372 #> 77: 2 30 0.088006372 #> 78: 2 30 0.088006372 #> 79: 2 30 0.088006372 #> 80: 2 30 0.088006372 #> 81: 2 30 0.088006372 #> 82: 0 32 0.024727916 #> 83: 0 32 0.024727916 #> 84: 0 32 0.024727916 #> 85: 1 31 0.045606289 #> 86: 2 30 0.061231889 #> 87: 0 32 0.015077998 #> 88: 2 30 0.041914334 #> 89: 2 30 0.041914334 #> 90: 3 29 0.051193356 #> 91: 0 32 0.009121258 #> 92: 0 32 0.009121258 #> 93: 0 32 0.009121258 #> 94: 1 31 0.019285199 #> 95: 0 32 0.005472755 #> 96: 0 32 0.005472755 #> 97: 1 31 0.007737122 #> 98: 0 32 0.001920171 #> 99: 0 32 0.001122178 #> Negative Present Negative Absent P-Value