Closed MingLi-929 closed 2 years ago
This pr is to fix a bug, according to #170. Here is the comfirmation. Download the narrowPeak file,broadPeak and gappedPeak file from MACS. And read these files by readPeakFile() and direactly way.
library(ChIPseeker) narrow <- readPeakFile("run_callpeak_narrow0_peaks.narrowPeak") narrow_test <- read.delim("run_callpeak_narrow0_peaks.narrowPeak", comment.char = "#",header = F) broad <- readPeakFile("run_callpeak_broad_peaks.broadPeak") broad_test <- read.delim("run_callpeak_broad_peaks.broadPeak", comment.char = "#",header = F) gapped <- readPeakFile("run_callpeak_broad_peaks.gappedPeak") gapped_test <- read.delim("run_callpeak_broad_peaks.gappedPeak", comment.char = "#",header = F)
Here is the comparison of narrowPeak file. 730 items in Granges obj and matrix.
> narrow GRanges object with 730 ranges and 7 metadata columns: seqnames ranges strand | V4 <Rle> <IRanges> <Rle> | <character> [1] chr22 17255467-17255847 * | run_callpeak_narrow0.. [2] chr22 17372665-17373263 * | run_callpeak_narrow0.. [3] chr22 17392236-17392676 * | run_callpeak_narrow0.. [4] chr22 17398274-17398699 * | run_callpeak_narrow0.. [5] chr22 17538969-17539492 * | run_callpeak_narrow0.. ... ... ... ... . ... [726] chr22 51060642-51061034 * | run_callpeak_narrow0.. [727] chr22 51129862-51130373 * | run_callpeak_narrow0.. [728] chr22 51170497-51171010 * | run_callpeak_narrow0.. [729] chr22 51195415-51195798 * | run_callpeak_narrow0.. [730] chr22 51213629-51213946 * | run_callpeak_narrow0.. V5 V6 V7 V8 V9 V10 <integer> <character> <numeric> <numeric> <numeric> <integer> [1] 214 . 13.2158 24.2291 21.4687 166 [2] 408 . 21.3866 44.0149 40.8560 283 [3] 866 . 38.6603 90.8119 86.6351 217 [4] 508 . 22.0952 54.2169 50.8226 203 [5] 428 . 19.5260 46.0327 42.8229 282 ... ... ... ... ... ... ... [726] 157 . 6.10754 18.3857 15.7468 184 [727] 346 . 13.83010 37.6338 34.6136 255 [728] 192 . 11.30450 21.9726 19.2590 226 [729] 103 . 7.70763 12.8618 10.3401 162 [730] 214 . 13.27340 24.1997 21.4401 141 ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths =========================================================================== > dim(narrow_test) [1] 730 10
Here is the comparison in broadPeak file. 745 items in Granges obj but 746 in matrix. Here comes the bug.
> broad GRanges object with 745 ranges and 6 metadata columns: seqnames ranges strand | run_callpeak_broad_peak_1 <Rle> <IRanges> <Rle> | <character> [1] chr22 17372665-17373263 * | run_callpeak_broad_p.. [2] chr22 17392235-17392676 * | run_callpeak_broad_p.. [3] chr22 17398271-17398728 * | run_callpeak_broad_p.. [4] chr22 17538929-17539492 * | run_callpeak_broad_p.. [5] chr22 17555766-17556245 * | run_callpeak_broad_p.. ... ... ... ... . ... [741] chr22 51060337-51061034 * | run_callpeak_broad_p.. [742] chr22 51129862-51130373 * | run_callpeak_broad_p.. [743] chr22 51170497-51171010 * | run_callpeak_broad_p.. [744] chr22 51195404-51195812 * | run_callpeak_broad_p.. [745] chr22 51213626-51213946 * | run_callpeak_broad_p.. X110 . X8.20787 X13.5941 X11.0752 <integer> <character> <numeric> <numeric> <numeric> [1] 175 . 11.0340 20.2366 17.5880 [2] 412 . 20.7017 44.4668 41.2894 [3] 246 . 12.9593 27.4385 24.6290 [4] 200 . 11.5619 22.7066 20.0028 [5] 321 . 15.8014 35.1451 32.1652 ... ... ... ... ... ... [741] 75 . 4.84068 9.96309 7.55174 [742] 197 . 10.23950 22.40530 19.70920 [743] 116 . 8.21861 14.12390 11.60230 [744] 47 . 4.86105 7.13422 4.78776 [745] 139 . 9.69485 16.53970 13.95900 ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths ============================================================================ > dim(broad_test) [1] 746 9
Here is the comparison in gappedPeak file. The same as the situation in broadPeak file. 745 items in Granges but 746 in matrix.
> gapped GRanges object with 745 ranges and 12 metadata columns: seqnames ranges strand | run_callpeak_broad_peak_1 <Rle> <IRanges> <Rle> | <character> [1] chr22 17372665-17373263 * | run_callpeak_broad_p.. [2] chr22 17392235-17392676 * | run_callpeak_broad_p.. [3] chr22 17398271-17398728 * | run_callpeak_broad_p.. [4] chr22 17538929-17539492 * | run_callpeak_broad_p.. [5] chr22 17555766-17556245 * | run_callpeak_broad_p.. ... ... ... ... . ... [741] chr22 51060337-51061034 * | run_callpeak_broad_p.. [742] chr22 51129862-51130373 * | run_callpeak_broad_p.. [743] chr22 51170497-51171010 * | run_callpeak_broad_p.. [744] chr22 51195404-51195812 * | run_callpeak_broad_p.. [745] chr22 51213626-51213946 * | run_callpeak_broad_p.. X110 . X17255466.1 X17255847.1 X0 <integer> <character> <integer> <integer> <integer> [1] 175 . 17372664 17373263 0 [2] 412 . 17392234 17392676 0 [3] 246 . 17398270 17398728 0 [4] 200 . 17538928 17539492 0 [5] 321 . 17555765 17556245 0 ... ... ... ... ... ... [741] 75 . 51060336 51061034 0 [742] 197 . 51129861 51130373 0 [743] 116 . 51170496 51171010 0 [744] 47 . 51195403 51195812 0 [745] 139 . 51213625 51213946 0 X1 X381 X0.1 X8.20787 X13.5941 X11.0752 <integer> <character> <character> <numeric> <numeric> <numeric> [1] 1 599 0 11.0340 20.2366 17.5880 [2] 2 1,441 0,1 20.7017 44.4668 41.2894 [3] 3 1,426,1 0,3,457 12.9593 27.4385 24.6290 [4] 2 1,524 0,40 11.5619 22.7066 20.0028 [5] 2 1,476 0,4 15.8014 35.1451 32.1652 ... ... ... ... ... ... ... [741] 2 1,393 0,305 4.84068 9.96309 7.55174 [742] 1 512 0 10.23950 22.40530 19.70920 [743] 1 514 0 8.21861 14.12390 11.60230 [744] 3 1,384,1 0,11,408 4.86105 7.13422 4.78776 [745] 2 1,318 0,3 9.69485 16.53970 13.95900 ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths ==================================================================================== > dim(gapped_test) [1] 746 15
This pr is to fix a bug, according to #170. Here is the comfirmation. Download the narrowPeak file,broadPeak and gappedPeak file from MACS. And read these files by readPeakFile() and direactly way.
Here is the comparison of narrowPeak file. 730 items in Granges obj and matrix.
Here is the comparison in broadPeak file. 745 items in Granges obj but 746 in matrix. Here comes the bug.
Here is the comparison in gappedPeak file. The same as the situation in broadPeak file. 745 items in Granges but 746 in matrix.