No overlaps or Enrichment in Results

[Sathish9]

I am using SNP data in regulatory regions to calculate enrichments. I am using the R package.
My Input data (hg38) looks like this:
GRanges object with 1800 ranges and 0 metadata columns:
seqnames ranges strand

[1] chr1 51851558-51851559 *
[2] chr1 51800569-51800570 *
[3] chr1 51825311-51825312 *
[4] chr1 51832478-51832479 *
[5] chr1 51845209-51845210 *

However, I am not getting any results.

  category nb.overlaps random.average mapped.peaks.ratio effect.size p.significance p.value q.significance q.value

TAL1 TAL1 0 0 0 NaN NA NA NA NA
GABPA GABPA 0 0 0 NaN NA NA NA NA
FOXP1 FOXP1 0 0 0 NaN NA NA NA NA
NME2 NME2 0 0 0 NaN NA NA NA NA
NRF1 NRF1 0 0 0 NaN NA NA NA NA
CTCF CTCF 0 0 0 NaN NA NA NA NA
e.significance e.value
TAL1 NA NA
GABPA NA NA
FOXP1 NA NA
NME2 NA NA
NRF1 NA NA
CTCF NA NA

I am not sure what I am doing wrong and would appreciate any feedback.

[MartinMestdagh]

Hi,
Can you provide a minimum reproducible example?

[Sathish9]

I used hg19 assembly.

setwd("/Users/uqsperiy/Brain_Data/")
library(ReMapEnrich)

Or download other versions

remapCatalog2018hg19 <- downloadRemapCatalog(demo.dir, version = "2018", assembly = "hg19")
remapCatalog <- bedToGranges(remapCatalog2018hg19)
print(remapCatalog)
query <- bedToGranges("./MDD/PGC_UKB_MDD_Remap_eQTL_5e-5_SNPs.bed")
enrichment.df <- enrichment(query, remapCatalog, byChrom = FALSE)
head(enrichment.df)

[Sathish9]

The bed file

chr1 52317230 52317231
chr1 52266241 52266242
chr1 52290983 52290984
chr1 52298150 52298151
chr1 52310881 52310882
chr1 52320558 52320559
chr1 52344413 52344414
chr1 67052163 67052164
chr1 67052608 67052609
chr1 67054079 67054080
chr1 67054080 67054081
chr1 67054906 67054907
chr1 67058022 67058023
chr1 67062125 67062126
chr1 67062884 67062885
chr1 67065910 67065911
chr1 67066029 67066030
chr1 67066554 67066555
chr1 67067368 67067369
chr1 67068111 67068112
chr1 67068239 67068240
chr1 67068536 67068537
chr1 67070380 67070381
chr1 67072030 67072031
chr1 67072975 67072976
chr1 67073313 67073314
chr1 67073565 67073566
chr1 67074176 67074177
chr1 67075574 67075575
chr1 67083670 67083671
chr1 67086110 67086111
chr1 67089219 67089220
chr1 67093017 67093018
chr1 67094335 67094336
chr1 67097852 67097853
chr1 67106076 67106077
chr1 67110515 67110516
chr1 67114308 67114309
chr1 67116230 67116231
chr1 67121000 67121001
chr1 67121131 67121132
chr1 67121363 67121364
chr1 67121433 67121434
chr1 67121633 67121634
chr1 67121662 67121663
chr1 67122551 67122552
chr1 67122564 67122565
chr1 67123056 67123057
chr1 67123458 67123459
chr1 67123741 67123742
chr1 67126584 67126585
chr1 67127366 67127367
chr1 67129253 67129254
chr1 67129481 67129482
chr1 67129790 67129791
chr1 67132261 67132262
chr1 67138366 67138367
chr1 67139666 67139667
chr1 67140722 67140723
chr1 67141948 67141949
chr1 67142285 67142286
chr1 67143054 67143055
chr1 67143333 67143334
chr1 67143367 67143368
chr1 67145321 67145322
chr1 67146816 67146817
chr1 67150279 67150280
chr1 67150810 67150811
chr1 67151184 67151185
chr1 67152498 67152499
chr1 72558137 72558138
chr1 72559739 72559740
chr1 72565459 72565460
chr1 72569612 72569613
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chr1 72573431 72573432
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chr1 72688502 72688503
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chr1 72951343 72951344
chr1 72953021 72953022
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chr1 176135784 176135785
chr1 176135991 176135992
chr1 176139562 176139563
chr1 176164864 176164865
chr1 176182721 176182722
chr1 176302096 176302097
chr1 176303203 176303204
chr1 176321146 176321147
chr1 176323425 176323426
chr3 49214065 49214066
chr3 49210731 49210732
chr3 49214302 49214303
chr3 49619492 49619493
chr3 49621993 49621994
chr3 49624064 49624065
chr3 49639802 49639803
chr3 49642026 49642027
chr3 49645208 49645209
chr3 49645457 49645458
chr3 49646980 49646981
chr3 49647403 49647404
chr3 49798863 49798864
chr3 49825368 49825369
chr3 49829652 49829653
chr5 87545317 87545318
chr5 87630768 87630769
chr6 26354099 26354100
chr6 26354246 26354247
chr6 26354779 26354780
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[MartinMestdagh]

hello, thanks you
i cant realize bedTogGranges with your file
can you tell me how many columns have you in your bedfile and dimension with
datafile <- bedImport(path.file)
dim(datafile)
class(datafile)
colnames(datafile)

[Sathish9]

Here it is:

datafile <- bedImport("./MDD/PGC_UKB_MDD_Remap_eQTL_5e-5_SNPs_hg38.bed")
dim(datafile)
[1] 1800 3
class(datafile)
[1] "data.frame"
colnames(datafile)
[1] "chrom" "chromStart" "chromEnd"

[MartinMestdagh]

thank you for your response
i will look at it and try to resolve the problem.
Can you try the annotate page on remap? http://remap.univ-amu.fr/annotate_page

[Sathish9]

I did that and I am getting an error:
"An error has occurred. Check your logs or contact the app author for clarification."