Fold enrichment value when running IDR with pvalue rank

[msantorsola]

Hi,

I performed IDR analysis on peaks called by MACS2 with the following command line:

idr --samples ${peakDir}/rep1_sorted_peaks.narrowPeak ${peakDir}/rep2_sorted_peaks.narrowPeak \ --input-file-type narrowPeak \ --rank p.value \ --output-file regular_model-idr \ --plot \ --log-output-file regular_model.idr.log

The IDR results show the peak list ranked for pvalue and set signalValue and qvalue to -1. Now, I would like to retrieve the signalValue (~fold enrichment) for each peak regions from original MACS2 output, i.e.

Chr	Start	End	Name	scaledIDR	Strand	signalValue	pvalue	qvalue	peak	globalIDR	localIDR	rep1_Start	rep1_End	rep1_signalValue	rep1_summit	rep2_Start	rep2_End	rep2_signalValue	rep2_summit	fold_enrichment_rep1	pvalue_1	fold_enrichment_rep2	pvalue_2
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.7965	8.68942	2.2494	11.32801
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.7965	8.68942	2.42635	18.19401
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.7965	8.68942	2.15729	14.41833
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.7965	8.68942	2.14088	13.07617
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.7965	8.68942	2.27126	17.29216
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.7965	8.68942	2.23416	22.68965
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.7965	8.68942	2.26469	20.03755
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.7965	8.68942	2.35859	25.66975
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	2.47086	30.05785	2.2494	11.32801
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	2.47086	30.05785	2.42635	18.19401
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	2.47086	30.05785	2.15729	14.41833
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	2.47086	30.05785	2.14088	13.07617
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	2.47086	30.05785	2.27126	17.29216
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	2.47086	30.05785	2.23416	22.68965
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	2.47086	30.05785	2.26469	20.03755
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	2.47086	30.05785	2.35859	25.66975
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.94094	13.9285	2.2494	11.32801
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.94094	13.9285	2.42635	18.19401
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.94094	13.9285	2.15729	14.41833
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.94094	13.9285	2.14088	13.07617
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501	1.94094	13.9285	2.27126	17.29216
...

and the related IDR merged peak

Chr	Start	End	Name	scaledIDR	Strand	signalValue	pvalue	qvalue	peak	globalIDR	localIDR	rep1_Start	rep1_End	rep1_signalValue	rep1_summit	rep2_Start	rep2_End	rep2_signalValue	rep2_summit
chr10	38815703	38818793	.	288	.	-1	8.68942	-1	2374	0.012076	0.695235	38815703	38818793	8.68942	1449	38815732	38818791	11.32801	1501

I notice that rep1_signalValue and rep2_signalValue fields report the min(pvalue) for each replicate, respectively, and the signalValue reports the min(pvalue) between the two replicates. How the value of the signalValue/fold_enrichment should be estimated for each IDR merged peak?