Import peaks in narrowPeak, broadPeak or bed format
One or more files to be imported. All files must be of the same type, i.e. narrow or broad
The type of peaks to be imported
A set of ranges to be excluded
A seqinfo object to be applied to the GRanges objects
How to handle conflicts if supplying a seqinfo object.
Defaults to pruning.mode = "coarse". Only "coarse" and "error" are
implemented. See seqinfo.
logical. Should the ranges be sorted during import
logical Set basename(x) as the name for each element of the GRangesList
glue syntax for naming list elements
Add the estimated peak centre. Ignored unless type = "narrow"
Place any values in the name column as range names within each file.
passed to sort
A GRangesList
Peaks are imported from narrowPeak, broadPeak or bed format as GenomicRanges objects.
If importing bed files, only the default 3-6 columns will imported.
fl <- system.file(
c("extdata/ER_1.narrowPeak", "extdata/ER_2.narrowPeak"),
package = "extraChIPs"
)
peaks <- importPeaks(fl)
peaks
#> GRangesList object of length 2:
#> $ER_1.narrowPeak
#> GRanges object with 10 ranges and 5 metadata columns:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> T47D_ER_E2_1_mapped_reads_peak_1 chr1 856458-856640 * | 56
#> T47D_ER_E2_1_mapped_reads_peak_2 chr1 1008550-1010075 * | 6357
#> T47D_ER_E2_1_mapped_reads_peak_3 chr1 1014771-1016015 * | 951
#> T47D_ER_E2_1_mapped_reads_peak_4 chr1 1051383-1051896 * | 655
#> T47D_ER_E2_1_mapped_reads_peak_5 chr1 1342664-1342846 * | 66
#> T47D_ER_E2_1_mapped_reads_peak_6 chr1 1368480-1368979 * | 225
#> T47D_ER_E2_1_mapped_reads_peak_7 chr1 1608098-1608345 * | 723
#> T47D_ER_E2_1_mapped_reads_peak_8 chr1 1790733-1790975 * | 77
#> T47D_ER_E2_1_mapped_reads_peak_9 chr1 1878927-1879257 * | 338
#> T47D_ER_E2_1_mapped_reads_peak_10 chr1 1900588-1900902 * | 225
#> signalValue pValue qValue peak
#> <numeric> <numeric> <numeric> <numeric>
#> T47D_ER_E2_1_mapped_reads_peak_1 5.65444 8.52782 5.65761 91
#> T47D_ER_E2_1_mapped_reads_peak_2 149.37155 641.42468 635.74786 662
#> T47D_ER_E2_1_mapped_reads_peak_3 33.45546 98.85455 95.12226 210
#> T47D_ER_E2_1_mapped_reads_peak_4 25.44500 69.13743 65.55376 182
#> T47D_ER_E2_1_mapped_reads_peak_5 6.12565 9.59455 6.68896 108
#> T47D_ER_E2_1_mapped_reads_peak_6 12.25129 25.77251 22.54826 133
#> T47D_ER_E2_1_mapped_reads_peak_7 27.32981 75.94558 72.32353 149
#> T47D_ER_E2_1_mapped_reads_peak_8 6.59685 10.69307 7.75227 115
#> T47D_ER_E2_1_mapped_reads_peak_9 16.02092 37.24069 33.88997 160
#> T47D_ER_E2_1_mapped_reads_peak_10 12.25129 25.77251 22.54826 169
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> $ER_2.narrowPeak
#> GRanges object with 10 ranges and 5 metadata columns:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> T47D_ER_E2_2_mapped_reads_peak_1 chr1 868541-868839 * | 97
#> T47D_ER_E2_2_mapped_reads_peak_2 chr1 1008607-1010057 * | 6050
#> T47D_ER_E2_2_mapped_reads_peak_3 chr1 1014770-1015980 * | 783
#> T47D_ER_E2_2_mapped_reads_peak_4 chr1 1051307-1051918 * | 959
#> T47D_ER_E2_2_mapped_reads_peak_5 chr1 1296000-1296181 * | 66
#> T47D_ER_E2_2_mapped_reads_peak_6 chr1 1310420-1310703 * | 55
#> T47D_ER_E2_2_mapped_reads_peak_7 chr1 1368372-1369009 * | 291
#> T47D_ER_E2_2_mapped_reads_peak_8 chr1 1608102-1608346 * | 648
#> T47D_ER_E2_2_mapped_reads_peak_9 chr1 1690460-1690641 * | 35
#> T47D_ER_E2_2_mapped_reads_peak_10 chr1 1878958-1879250 * | 144
#> signalValue pValue qValue peak
#> <numeric> <numeric> <numeric> <numeric>
#> T47D_ER_E2_2_mapped_reads_peak_1 7.42145 12.78537 9.77580 165
#> T47D_ER_E2_2_mapped_reads_peak_2 141.93524 610.62402 605.03973 605
#> T47D_ER_E2_2_mapped_reads_peak_3 28.75812 82.09051 78.39533 179
#> T47D_ER_E2_2_mapped_reads_peak_4 33.39653 99.75146 95.96765 327
#> T47D_ER_E2_2_mapped_reads_peak_5 5.89933 9.56727 6.65018 135
#> T47D_ER_E2_2_mapped_reads_peak_6 5.56609 8.38709 5.51349 139
#> T47D_ER_E2_2_mapped_reads_peak_7 14.37906 32.45039 29.12307 395
#> T47D_ER_E2_2_mapped_reads_peak_8 25.04739 68.45815 64.84392 145
#> T47D_ER_E2_2_mapped_reads_peak_9 4.63841 6.38478 3.59695 120
#> T47D_ER_E2_2_mapped_reads_peak_10 9.27681 17.60511 14.49095 136
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>