Segregate input sequences into common and unique groups
Source:R/segregate_seqs.R
segregate_seqs.RdThis function takes two sets of sequences and segregates them into common and unique sequences. The common sequences are sequences that are present in both sets of sequences. The unique sequences are sequences that are present in only one of the sets of sequences.
Value
A list containing the common sequences and unique sequences for each
set of sequences. The list contains the following GRanges objects:
common_seqs1: Common sequences inseqs1common_seqs2: Common sequences inseqs2unique_seqs1: Unique sequences inseqs1unique_seqs2: Unique sequences inseqs2
Details
Sequences are considered common if their base pairs align in any position, even if they vary in length. Consequently, while the number of common sequences remains consistent between both sets, but the length and composition of these sequences may differ. As a result, the function returns distinct sets of common sequences for each input set of sequences.
Examples
data("CTCF_ChIP_peaks", package = "MotifPeeker")
data("CTCF_TIP_peaks", package = "MotifPeeker")
seqs1 <- CTCF_ChIP_peaks
seqs2 <- CTCF_TIP_peaks
res <- segregate_seqs(seqs1, seqs2)
print(res)
#> $common_seqs1
#> GRanges object with 127 ranges and 7 metadata columns:
#> seqnames ranges strand | name
#> <Rle> <IRanges> <Rle> | <character>
#> ChIPseq_peak_3 chr10 66180787-66181041 * | ChIPseq_peak_3
#> ChIPseq_peak_6 chr10 66455384-66455636 * | ChIPseq_peak_6
#> ChIPseq_peak_7 chr10 66586154-66586345 * | ChIPseq_peak_7
#> ChIPseq_peak_8 chr10 66627231-66627517 * | ChIPseq_peak_8
#> ChIPseq_peak_9 chr10 66925870-66926137 * | ChIPseq_peak_9
#> ... ... ... ... . ...
#> ChIPseq_peak_199 chr10 74081271-74081544 * | ChIPseq_peak_199
#> ChIPseq_peak_200 chr10 74103609-74103897 * | ChIPseq_peak_200
#> ChIPseq_peak_202 chr10 74153172-74153433 * | ChIPseq_peak_202
#> ChIPseq_peak_206 chr10 74266052-74266297 * | ChIPseq_peak_206
#> ChIPseq_peak_207 chr10 74419925-74420183 * | ChIPseq_peak_207
#> score signalValue pValue qValue peak
#> <numeric> <numeric> <numeric> <numeric> <integer>
#> ChIPseq_peak_3 250 13.6027 28.6276 25.0595 117
#> ChIPseq_peak_6 398 17.2191 43.6096 39.8530 112
#> ChIPseq_peak_7 245 13.3070 28.1324 24.5738 86
#> ChIPseq_peak_8 556 20.9281 59.6139 55.6729 146
#> ChIPseq_peak_9 635 22.0495 67.6284 63.5924 131
#> ... ... ... ... ... ...
#> ChIPseq_peak_199 956 26.9507 100.0720 95.6116 144
#> ChIPseq_peak_200 335 15.2085 37.2591 33.5791 116
#> ChIPseq_peak_202 430 16.4674 46.8334 43.0387 136
#> ChIPseq_peak_206 613 21.7807 65.4013 61.3937 110
#> ChIPseq_peak_207 457 18.4381 49.5552 45.7299 134
#> summit
#> <integer>
#> ChIPseq_peak_3 66180904
#> ChIPseq_peak_6 66455496
#> ChIPseq_peak_7 66586240
#> ChIPseq_peak_8 66627377
#> ChIPseq_peak_9 66926001
#> ... ...
#> ChIPseq_peak_199 74081415
#> ChIPseq_peak_200 74103725
#> ChIPseq_peak_202 74153308
#> ChIPseq_peak_206 74266162
#> ChIPseq_peak_207 74420059
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> $common_seqs2
#> GRanges object with 127 ranges and 7 metadata columns:
#> seqnames ranges strand | name score
#> <Rle> <IRanges> <Rle> | <character> <numeric>
#> TIPseq_peak_1 chr10 66180800-66181033 * | TIPseq_peak_1 73
#> TIPseq_peak_2 chr10 66455342-66455626 * | TIPseq_peak_2 99
#> TIPseq_peak_3 chr10 66586093-66586239 * | TIPseq_peak_3 63
#> TIPseq_peak_4 chr10 66627203-66627536 * | TIPseq_peak_4 122
#> TIPseq_peak_5 chr10 66925844-66926200 * | TIPseq_peak_5 234
#> ... ... ... ... . ... ...
#> TIPseq_peak_171 chr10 74081300-74081610 * | TIPseq_peak_171 44
#> TIPseq_peak_172 chr10 74103638-74103872 * | TIPseq_peak_172 75
#> TIPseq_peak_174 chr10 74153189-74153455 * | TIPseq_peak_174 100
#> TIPseq_peak_180 chr10 74265994-74266358 * | TIPseq_peak_180 142
#> TIPseq_peak_181 chr10 74419929-74420132 * | TIPseq_peak_181 101
#> signalValue pValue qValue peak summit
#> <numeric> <numeric> <numeric> <integer> <integer>
#> TIPseq_peak_1 7.26312 10.98040 7.31252 50 66180850
#> TIPseq_peak_2 8.68181 13.84590 9.92037 142 66455484
#> TIPseq_peak_3 6.18211 9.90174 6.32942 80 66586173
#> TIPseq_peak_4 9.80905 16.47740 12.27160 114 66627317
#> TIPseq_peak_5 14.14660 28.95280 23.43290 174 66926018
#> ... ... ... ... ... ...
#> TIPseq_peak_171 5.66751 7.86457 4.47255 134 74081434
#> TIPseq_peak_172 7.39208 11.22360 7.53561 121 74103759
#> TIPseq_peak_174 7.91950 14.01050 10.06950 65 74153254
#> TIPseq_peak_180 10.25590 18.75230 14.29350 180 74266174
#> TIPseq_peak_181 8.69840 14.05790 10.11420 58 74419987
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> $unique_seqs1
#> GRanges object with 82 ranges and 7 metadata columns:
#> seqnames ranges strand | name
#> <Rle> <IRanges> <Rle> | <character>
#> ChIPseq_peak_1 chr10 65672891-65673094 * | ChIPseq_peak_1
#> ChIPseq_peak_2 chr10 66112133-66112279 * | ChIPseq_peak_2
#> ChIPseq_peak_4 chr10 66215124-66215282 * | ChIPseq_peak_4
#> ChIPseq_peak_5 chr10 66277566-66277829 * | ChIPseq_peak_5
#> ChIPseq_peak_12 chr10 67476285-67476431 * | ChIPseq_peak_12
#> ... ... ... ... . ...
#> ChIPseq_peak_203 chr10 74213629-74213890 * | ChIPseq_peak_203
#> ChIPseq_peak_204 chr10 74234663-74234817 * | ChIPseq_peak_204
#> ChIPseq_peak_205 chr10 74244202-74244399 * | ChIPseq_peak_205
#> ChIPseq_peak_208 chr10 74738977-74739145 * | ChIPseq_peak_208
#> ChIPseq_peak_209 chr10 74826600-74826822 * | ChIPseq_peak_209
#> score signalValue pValue qValue peak
#> <numeric> <numeric> <numeric> <numeric> <integer>
#> ChIPseq_peak_1 132 9.71581 16.61240 13.21760 91
#> ChIPseq_peak_2 47 5.72046 7.95781 4.74195 77
#> ChIPseq_peak_4 98 7.90847 13.19130 9.85816 52
#> ChIPseq_peak_5 343 16.08460 38.04630 34.35700 126
#> ChIPseq_peak_12 71 6.85832 10.48160 7.19900 76
#> ... ... ... ... ... ...
#> ChIPseq_peak_203 776 25.89270 81.79150 77.60160 120
#> ChIPseq_peak_204 73 6.97553 10.67840 7.39263 80
#> ChIPseq_peak_205 144 9.44644 17.88500 14.46760 91
#> ChIPseq_peak_208 66 6.52919 9.93714 6.66903 96
#> ChIPseq_peak_209 192 11.78170 22.77100 19.28080 112
#> summit
#> <integer>
#> ChIPseq_peak_1 65672982
#> ChIPseq_peak_2 66112210
#> ChIPseq_peak_4 66215176
#> ChIPseq_peak_5 66277692
#> ChIPseq_peak_12 67476361
#> ... ...
#> ChIPseq_peak_203 74213749
#> ChIPseq_peak_204 74234743
#> ChIPseq_peak_205 74244293
#> ChIPseq_peak_208 74739073
#> ChIPseq_peak_209 74826712
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> $unique_seqs2
#> GRanges object with 57 ranges and 7 metadata columns:
#> seqnames ranges strand | name score
#> <Rle> <IRanges> <Rle> | <character> <numeric>
#> TIPseq_peak_7 chr10 67284781-67284927 * | TIPseq_peak_7 42
#> TIPseq_peak_10 chr10 67531067-67531356 * | TIPseq_peak_10 59
#> TIPseq_peak_13 chr10 67779549-67779763 * | TIPseq_peak_13 48
#> TIPseq_peak_16 chr10 67838030-67838183 * | TIPseq_peak_16 34
#> TIPseq_peak_17 chr10 67849319-67849603 * | TIPseq_peak_17 83
#> ... ... ... ... . ... ...
#> TIPseq_peak_176 chr10 74190108-74190333 * | TIPseq_peak_176 82
#> TIPseq_peak_177 chr10 74224190-74224510 * | TIPseq_peak_177 78
#> TIPseq_peak_178 chr10 74231494-74231667 * | TIPseq_peak_178 78
#> TIPseq_peak_179 chr10 74243885-74244038 * | TIPseq_peak_179 64
#> TIPseq_peak_182 chr10 74826265-74826421 * | TIPseq_peak_182 45
#> signalValue pValue qValue peak summit
#> <numeric> <numeric> <numeric> <integer> <integer>
#> TIPseq_peak_7 5.16484 7.66518 4.29365 42 67284823
#> TIPseq_peak_10 6.40051 9.51973 5.98156 84 67531151
#> TIPseq_peak_13 5.32656 8.31207 4.88917 74 67779623
#> TIPseq_peak_16 4.47387 6.76965 3.47941 125 67838155
#> TIPseq_peak_17 7.77252 12.07180 8.32041 104 67849423
#> ... ... ... ... ... ...
#> TIPseq_peak_176 7.72798 11.99220 8.24690 144 74190252
#> TIPseq_peak_177 7.30707 11.51720 7.81021 128 74224318
#> TIPseq_peak_178 7.55650 11.53680 7.82873 111 74231605
#> TIPseq_peak_179 6.73978 10.04360 6.45615 47 74243932
#> TIPseq_peak_182 5.72697 7.96895 4.56751 20 74826285
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>