This function reads a MACS2/3 narrowPeak or SEACR BED peak file and returns a GRanges object with the peak coordinates and summit.
Arguments
- peak_file
A character string with the path to the peak file, or a GRanges object created using
read_peak_file().- file_format
A character string specifying the format of the peak file.
"narrowpeak": MACS2/3 narrowPeak format."bed": SEACR BED format.
- verbose
A logical indicating whether to print messages.
Value
A GRanges-class object with the peak coordinates and summit.
Details
The summit column is the absolute genomic position of the peak, which is relative to the start position of the sequence range. For SEACR BED files, the summit column is calculated as the midpoint of the max signal region.
See also
GRanges-class for more information on GRanges objects.
Examples
macs3_peak_file <- system.file("extdata", "CTCF_ChIP_peaks.narrowPeak",
package = "MotifPeeker")
macs3_peak_read <- read_peak_file(macs3_peak_file)
macs3_peak_read
#> GRanges object with 209 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_3 chr10 66180787-66181041 * | ChIPseq_peak_3
#> ChIPseq_peak_4 chr10 66215124-66215282 * | ChIPseq_peak_4
#> ChIPseq_peak_5 chr10 66277566-66277829 * | ChIPseq_peak_5
#> ... ... ... ... . ...
#> ChIPseq_peak_205 chr10 74244202-74244399 * | ChIPseq_peak_205
#> ChIPseq_peak_206 chr10 74266052-74266297 * | ChIPseq_peak_206
#> ChIPseq_peak_207 chr10 74419925-74420183 * | ChIPseq_peak_207
#> 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_3 250 13.60270 28.62760 25.05950 117
#> ChIPseq_peak_4 98 7.90847 13.19130 9.85816 52
#> ChIPseq_peak_5 343 16.08460 38.04630 34.35700 126
#> ... ... ... ... ... ...
#> ChIPseq_peak_205 144 9.44644 17.88500 14.46760 91
#> ChIPseq_peak_206 613 21.78070 65.40130 61.39370 110
#> ChIPseq_peak_207 457 18.43810 49.55520 45.72990 134
#> 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_3 66180904
#> ChIPseq_peak_4 66215176
#> ChIPseq_peak_5 66277692
#> ... ...
#> ChIPseq_peak_205 74244293
#> ChIPseq_peak_206 74266162
#> ChIPseq_peak_207 74420059
#> ChIPseq_peak_208 74739073
#> ChIPseq_peak_209 74826712
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths