GRangesList of peaks and SummarizedExperiment of counts All were saved during initial vignette preparation at https://github.com/smped/extraChIPs_vignette/blob/main/differential_signal_fixed.Rmd
An object of class RangedSummarizedExperiment with 188 rows and 6 columns.
An object of class CompressedGRangesList of length 6.
data(se)
se
#> class: RangedSummarizedExperiment
#> dim: 188 6
#> metadata(2): final.ext param
#> assays(1): counts
#> rownames: NULL
#> rowData names(4): E2 E2DHT n union_peak
#> colnames(6): SRR8315180 SRR8315181 ... SRR8315184 SRR8315185
#> colData names(4): bam.files totals ext rlen
data(peaks)
peaks
#> GRangesList object of length 6:
#> $SRR8315180_peaks.narrowPeak
#> GRanges object with 123 ranges and 5 metadata columns:
#> seqnames ranges strand | score signalValue
#> <Rle> <IRanges> <Rle> | <numeric> <numeric>
#> SRR8315180_peak_698 chr10 43048224-43048487 * | 251 13.91781
#> SRR8315180_peak_699 chr10 43521883-43522126 * | 223 12.88686
#> SRR8315180_peak_700 chr10 43540200-43540384 * | 58 6.18569
#> SRR8315180_peak_701 chr10 43606308-43606517 * | 92 7.73212
#> SRR8315180_peak_702 chr10 44092187-44092576 * | 251 13.91781
#> ... ... ... ... . ... ...
#> SRR8315180_peak_819 chr10 95796039-95796377 * | 434 18.67842
#> SRR8315180_peak_820 chr10 96089595-96089749 * | 25 4.32096
#> SRR8315180_peak_821 chr10 99097150-99097384 * | 196 9.02984
#> SRR8315180_peak_822 chr10 99168353-99168578 * | 48 5.67022
#> SRR8315180_peak_823 chr10 99331430-99331686 * | 210 10.70668
#> pValue qValue peak
#> <numeric> <numeric> <numeric>
#> SRR8315180_peak_698 29.15643 25.19601 117
#> SRR8315180_peak_699 26.25515 22.33688 125
#> SRR8315180_peak_700 9.37883 5.87296 98
#> SRR8315180_peak_701 12.90188 9.27326 110
#> SRR8315180_peak_702 29.15643 25.19601 214
#> ... ... ... ...
#> SRR8315180_peak_819 47.62759 43.44466 186
#> SRR8315180_peak_820 5.88899 2.58967 6
#> SRR8315180_peak_821 23.51470 19.64532 109
#> SRR8315180_peak_822 8.26998 4.82385 153
#> SRR8315180_peak_823 24.91666 21.02332 191
#> -------
#> seqinfo: 25 sequences from GRCh37 genome
#>
#> ...
#> <5 more elements>