Entering edit mode
So I have already performed this action before with the same bed file with no problem and now when I simply copy the same commands another error appears. I am not sure what the error is talking about, any ideas? Thanks.
> bed <- as.data.frame(read.table("overlap_flag_coordinates_with_r_duplicates_removed.bed",header = FALSE, sep="\t",stringsAsFactors=FALSE, quote=""))
> print(bed)
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
1 chr1 903734 904216 split_on_flag_rep2_peak_15 42 . 4.59529 6.68330 4.24517 64
2 chr1 912653 912938 split_on_flag_rep2_peak_22 27 . 3.29425 4.79185 2.77313 189
3 chr1 913579 913927 split_on_flag_rep2_peak_23 38 . 4.80347 6.12447 3.80320 244
4 chr1 916913 917442 split_on_flag_rep2_peak_26 50 . 4.35974 7.66459 5.03850 93
5 chr1 917590 918117 split_on_flag_rep2_peak_27 83 . 5.57745 11.79668 8.33518 433
6 chr1 922128 922420 split_on_flag_rep2_peak_32 38 . 4.53120 6.12447 3.80320 204
7 chr1 938767 939240 split_on_flag_rep2_peak_44 58 . 5.63120 8.68049 5.85552 398
8 chr1 940569 941178 split_on_flag_rep2_peak_47 61 . 5.89254 9.09404 6.17741 226
9 chr1 967494 968383 split_on_flag_rep2_peak_51 27 . 3.29425 4.79185 2.77313 785
10 chr1 983793 984073 split_on_flag_rep2_peak_56 58 . 5.63120 8.68049 5.85552 55
11 chr1 1064104 1064725 split_on_flag_rep2_peak_72 42 . 3.73134 6.60524 4.21172 54
12 chr1 1068405 1068758 split_on_flag_rep2_peak_74 49 . 5.28030 7.55213 4.94117 74
13 chr1 1069660 1070580 split_on_flag_rep2_peak_76 102 . 7.23364 14.21410 10.25889 367
14 chr1 1117487 1117897 split_on_flag_rep2_peak_86 61 . 6.16481 9.09404 6.17741 236
15 chr1 1121720 1122220 split_on_flag_rep2_peak_90 123 . 9.01154 16.81533 12.32594 397
16 chr1 1130274 1130554 split_on_flag_rep2_peak_100 112 . 8.64179 15.45685 11.23009 178
17 chr1 1136461 1136703 split_on_flag_rep2_peak_108 35 . 4.59043 5.81492 3.59353 151
18 chr1 1140759 1140964 split_on_flag_rep2_peak_110 45 . 5.07574 7.07820 4.53636 82
19 chr1 1148471 1148827 split_on_flag_rep2_peak_118 69 . 5.12081 10.08017 6.98827 59
20 chr1 1156950 1157148 split_on_flag_rep2_peak_126 53 . 5.62027 8.06901 5.36720 90
21 chr1 1210192 1210606 split_on_flag_rep2_peak_167 62 . 5.69381 9.20763 6.27269 282
22 chr1 1291617 1291923 split_on_flag_rep2_peak_176 53 . 5.62027 8.06901 5.36720 235
23 chr1 1304443 1304781 split_on_flag_rep2_peak_177 144 . 9.97656 19.53761 14.42307 226
24 chr1 1348122 1348313 split_on_flag_rep2_peak_187 37 . 4.58563 5.96864 3.70799 151
25 chr1 1430370 1430949 split_on_flag_rep2_peak_207 94 . 7.62726 13.21828 9.47143 470
26 chr1 1441128 1442007 split_on_flag_rep2_peak_217 56 . 5.20414 8.41215 5.63397 265
27 chr1 1444032 1444313 split_on_flag_rep2_peak_221 38 . 4.53120 6.12447 3.80320 93
28 chr1 1455282 1455981 split_on_flag_rep2_peak_228 42 . 4.59529 6.68330 4.24517 606
29 chr1 1459234 1459499 split_on_flag_rep2_peak_231 30 . 4.25893 5.21123 3.08267 48
30 chr1 1578655 1578898 split_on_flag_rep2_peak_246 52 . 5.52933 7.93085 5.26537 133
31 chr1 1600442 1601124 split_on_flag_rep2_peak_263 110 . 8.49332 15.22205 11.06264 281
32 chr1 1907388 1907713 split_on_flag_rep2_peak_295 38 . 4.53120 6.12447 3.80320 30
33 chr1 1919784 1920559 split_on_flag_rep2_peak_302 78 . 6.01594 11.20838 7.84588 66
34 chr1 1937596 1937877 split_on_flag_rep2_peak_318 57 . 4.94853 8.52716 5.72150 49
35 chr1 1947476 1947772 split_on_flag_rep2_peak_328 44 . 4.05532 6.90630 4.42478 215
36 chr1 1951867 1952046 split_on_flag_rep2_peak_330 53 . 5.24104 8.06021 5.36720 88
37 chr1 1964284 1964419 split_on_flag_rep2_peak_342 31 . 4.27238 5.35210 3.19946 86
38 chr1 1965506 1966608 split_on_flag_rep2_peak_344 65 . 6.08193 9.59291 6.56973 982
39 chr1 1991183 1991354 split_on_flag_rep2_peak_362 17 . 2.83762 3.53412 1.78672 82
40 chr1 2015482 2015822 split_on_flag_rep2_peak_379 41 . 4.58358 6.48253 4.10451 63
41 chr1 2020501 2020839 split_on_flag_rep2_peak_387 42 . 4.58002 6.65913 4.24517 242
42 chr1 2045114 2045369 split_on_flag_rep2_peak_417 53 . 4.09665 7.99138 5.31981 125
43 chr1 2049192 2050077 split_on_flag_rep2_peak_421 147 . 9.99723 19.95232 14.76748 597
44 chr1 2209463 2210427 split_on_flag_rep2_peak_449 66 . 5.98636 9.67487 6.63819 74
45 chr1 2335696 2336115 split_on_flag_rep2_peak_482 35 . 4.59043 5.81492 3.59353 335
46 chr1 2342957 2343856 split_on_flag_rep2_peak_488 42 . 4.59529 6.68330 4.24517 825
47 chr1 2435344 2435598 split_on_flag_rep2_peak_517 32 . 4.34180 5.45328 3.28697 131
48 chr1 2437876 2438479 split_on_flag_rep2_peak_519 61 . 6.16481 9.09404 6.17741 528
49 chr1 2803485 2804203 split_on_flag_rep2_peak_537 59 . 5.21682 8.77902 5.93386 251
50 chr1 2810331 2810656 split_on_flag_rep2_peak_545 53 . 5.62027 8.06901 5.36720 80
51 chr1 2814511 2815043 split_on_flag_rep2_peak_551 93 . 7.53890 13.07700 9.37274 96
52 chr1 2815551 2815946 split_on_flag_rep2_peak_553 84 . 7.23378 11.89780 8.41582 296
53 chr1 2840559 2840783 split_on_flag_rep2_peak_575 37 . 4.69805 5.97127 3.70898 148
54 chr1 2860563 2861058 split_on_flag_rep2_peak_586 105 . 8.34295 14.65639 10.57929 382
55 chr1 2868563 2868845 split_on_flag_rep2_peak_596 70 . 6.03183 10.13394 7.03485 212
56 chr1 2887599 2888280 split_on_flag_rep2_peak_614 91 . 7.41012 12.87080 9.18740 255
57 chr1 2933899 2934034 split_on_flag_rep2_peak_658 39 . 4.58790 6.33154 3.97100 64
58 chr1 2942642 2943313 split_on_flag_rep2_peak_662 42 . 4.39234 6.68330 4.24517 498
59 chr1 2947108 2947275 split_on_flag_rep2_peak_666 42 . 4.59529 6.68330 4.24517 102
60 chr1 2950936 2951195 split_on_flag_rep2_peak_671 78 . 6.70934 11.23720 7.84588 100
61 chr1 2969892 2970328 split_on_flag_rep2_peak_681 45 . 5.07574 7.07820 4.53636 318
62 chr1 2980213 2980765 split_on_flag_rep2_peak_693 96 . 7.79842 13.49155 9.68812 129
63 chr1 2983442 2983609 split_on_flag_rep2_peak_696 45 . 5.07574 7.07820 4.53636 97
64 chr1 2988290 2988600 split_on_flag_rep2_peak_700 52 . 5.52933 7.93085 5.26537 192
65 chr1 3002861 3005047 split_on_flag_rep2_peak_706 104 . 7.78720 14.49067 10.49436 1955
66 chr1 3021472 3021628 split_on_flag_rep2_peak_716 65 . 5.08963 9.54463 6.52471 85
67 chr1 3026682 3026842 split_on_flag_rep2_peak_720 42 . 4.59529 6.68330 4.24517 50
68 chr1 3033561 3033699 split_on_flag_rep2_peak_728 47 . 4.80562 7.36005 4.78056 78
69 chr1 3349134 3349821 split_on_flag_rep2_peak_768 98 . 6.70868 13.63944 9.80151 580
70 chr1 3402496 3403030 split_on_flag_rep2_peak_782 83 . 5.57745 11.79668 8.33518 424
71 chr1 3423905 3424175 split_on_flag_rep2_peak_792 29 . 3.98644 5.08049 2.98889 203
72 chr1 3424303 3424785 split_on_flag_rep2_peak_793 42 . 5.11082 6.73404 4.28459 402
73 chr1 3442262 3442759 split_on_flag_rep2_peak_797 44 . 4.20753 6.90630 4.42478 215
74 chr1 3452088 3453048 split_on_flag_rep2_peak_803 110 . 8.23313 15.22205 11.06264 884
75 chr1 3459086 3459343 split_on_flag_rep2_peak_808 29 . 3.98644 5.08049 2.98889 171
76 chr1 3484119 3484433 split_on_flag_rep2_peak_824 54 . 5.32620 8.19604 5.47686 254
77 chr1 3535806 3536141 split_on_flag_rep2_peak_844 23 . 3.98667 4.34251 2.38194 65
78 chr1 3565488 3565973 split_on_flag_rep2_peak_862 42 . 4.59529 6.68330 4.24517 53
79 chr1 3652091 3652233 split_on_flag_rep2_peak_883 51 . 5.28599 7.75839 5.10916 61
80 chr1 3672004 3672154 split_on_flag_rep2_peak_891 42 . 4.59529 6.68330 4.24517 36
81 chr1 3702654 3703353 split_on_flag_rep2_peak_903 56 . 5.00119 8.41215 5.63397 393
82 chr1 3717594 3718024 split_on_flag_rep2_peak_908 45 . 5.34801 7.07820 4.53636 307
83 chr1 3746410 3746893 split_on_flag_rep2_peak_912 45 . 4.79342 6.99517 4.50186 382
84 chr1 3752410 3752776 split_on_flag_rep2_peak_914 53 . 4.77213 8.01736 5.33764 76
85 chr1 3755456 3755699 split_on_flag_rep2_peak_918 23 . 3.32663 4.34703 2.38354 197
86 chr1 3799892 3800224 split_on_flag_rep2_peak_929 84 . 7.01248 11.96289 8.47530 102
87 chr1 3906088 3906367 split_on_flag_rep2_peak_943 49 . 4.78230 7.50674 4.91519 87
88 chr1 3907607 3908194 split_on_flag_rep2_peak_945 77 . 6.82839 10.99833 7.73167 476
89 chr1 3910048 3910293 split_on_flag_rep2_peak_947 57 . 5.13427 8.52716 5.72150 79
90 chr1 3928694 3928878 split_on_flag_rep2_peak_956 74 . 6.45327 10.67549 7.46693 100
91 chr1 3939829 3940330 split_on_flag_rep2_peak_961 42 . 4.58002 6.65913 4.24517 184
92 chr1 3943899 3944176 split_on_flag_rep2_peak_965 94 . 6.80506 13.15166 9.43232 89
93 chr1 3957979 3958476 split_on_flag_rep2_peak_973 49 . 4.79824 7.53305 4.92334 99
94 chr1 3981391 3981675 split_on_flag_rep2_peak_984 45 . 4.94615 7.04170 4.53636 198
95 chr1 3982956 3983116 split_on_flag_rep2_peak_986 78 . 6.21889 11.20838 7.84588 82
96 chr1 4000019 4000219 split_on_flag_rep2_peak_994 47 . 3.85311 7.28745 4.72162 112
97 chr1 4002877 4003015 split_on_flag_rep2_peak_997 41 . 4.94105 6.48738 4.10793 57
98 chr1 4004015 4004383 split_on_flag_rep2_peak_999 77 . 6.69403 11.05501 7.78133 86
99 chr1 4004654 4005310 split_on_flag_rep2_peak_1000 38 . 3.90311 6.17367 3.83231 63
100 chr1 4010883 4011262 split_on_flag_rep2_peak_1004 49 . 4.79824 7.53305 4.92334 270
[ reached 'max' / getOption("max.print") -- omitted 19800 rows ]
> gr1 <- toGRanges(bed, format="BED", header=FALSE)
Error in (function (data, colNames = NULL, format = "", ...) :
colname must contain space/seqnames, start and end.
sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPpeakAnno_3.26.4 GenomicRanges_1.44.0 GenomeInfoDb_1.28.4 IRanges_2.26.0
[5] S4Vectors_0.30.2 BiocGenerics_0.38.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.24.0 bitops_1.0-7 matrixStats_0.61.0
[4] bit64_4.0.5 filelock_1.0.2 progress_1.2.2
[7] httr_1.4.2 InteractionSet_1.20.0 tools_4.1.1
[10] utf8_1.2.2 R6_2.5.1 colorspace_2.0-2
[13] DBI_1.1.2 lazyeval_0.2.2 tidyselect_1.1.1
[16] prettyunits_1.1.1 bit_4.0.4 curl_4.3.2
[19] compiler_4.1.1 VennDiagram_1.7.1 graph_1.70.0
[22] cli_3.1.1 Biobase_2.52.0 formatR_1.11
[25] xml2_1.3.3 DelayedArray_0.18.0 rtracklayer_1.52.1
[28] scales_1.1.1 RBGL_1.68.0 rappdirs_0.3.3
[31] stringr_1.4.0 digest_0.6.29 Rsamtools_2.8.0
[34] XVector_0.32.0 pkgconfig_2.0.3 MatrixGenerics_1.4.3
[37] BSgenome_1.60.0 regioneR_1.24.0 dbplyr_2.1.1
[40] fastmap_1.1.0 ensembldb_2.16.4 rlang_1.0.0
[43] rstudioapi_0.13 RSQLite_2.2.9 BiocIO_1.2.0
[46] generics_0.1.2 BiocParallel_1.26.2 dplyr_1.0.7
[49] RCurl_1.98-1.5 magrittr_2.0.2 GenomeInfoDbData_1.2.6
[52] futile.logger_1.4.3 Matrix_1.3-4 munsell_0.5.0
[55] Rcpp_1.0.8 fansi_1.0.2 lifecycle_1.0.1
[58] stringi_1.7.6 yaml_2.2.2 MASS_7.3-54
[61] SummarizedExperiment_1.22.0 zlibbioc_1.38.0 BiocFileCache_2.0.0
[64] grid_4.1.1 blob_1.2.2 crayon_1.4.2
[67] lattice_0.20-44 splines_4.1.1 Biostrings_2.60.2
[70] multtest_2.48.0 GenomicFeatures_1.44.2 hms_1.1.1
[73] KEGGREST_1.32.0 pillar_1.7.0 rjson_0.2.21
[76] biomaRt_2.48.3 futile.options_1.0.1 XML_3.99-0.8
[79] glue_1.6.1 lambda.r_1.2.4 png_0.1-7
[82] vctrs_0.3.8 gtable_0.3.0 purrr_0.3.4
[85] assertthat_0.2.1 cachem_1.0.6 ggplot2_3.3.5
[88] restfulr_0.0.13 AnnotationFilter_1.16.0 survival_3.2-11
[91] tibble_3.1.6 GenomicAlignments_1.28.0 AnnotationDbi_1.54.1
[94] memoise_2.0.1 ellipsis_0.3.2
Thanks for your help again. Setting up the format to narrowPeak worked, but only when I read the bed file via toGRanges() directly. Your suggestion about follow-up questions is also noted.