Estimation of the fold enrichment value when running IDR with pvalue as ranking measure

[Mariangela]

Hi,

I performed IDR analysis on MACS2 peaks with the `pvalue` as ranking measure

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 output show the peak list ranked for pvalue but set the signalValue and qvalue to -1

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

So, I need to retrieve the signalValue (~fold enrichment) for each peak regions from MACS2 narrowPeak file

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
...

but 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?

Can I use the sum of fold enrichment values of the two replicates and then the average among the multiple calls for each IDR merged peak?

Thanks

Mariangela