Question

diffHic: Error while counting in predefined regions

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manjulathimma • 0

@manjulathimma-11250

Last seen 8.1 years ago

Hi Aaron, I am trying to count interacting fragments in pre-defined regions.

But there seems to an error.

redata <- connectCounts(input, hs.param, regions=gene.body)
Error in connectCounts(input, hs.param, regions = gene.body) :
chromosome present in regions and not in fragments
In addition: Warning message:
In connectCounts(input, hs.param, regions = gene.body) :
stranded region ranges have no interpretation, coercing unstrandedness
> input
[1] "/Users/thimmamp/temp_tobe_deleted/HiCMapped/HepG2_trimmed.h5" "/Users/thimmamp/temp_tobe_deleted/HiCMapped/Ago1_trimmed.h5"

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.24.5                  AnnotationDbi_1.34.4                    BiocInstaller_1.22.3                    diffHic_1.4.3
[6] InteractionSet_1.0.4                    SummarizedExperiment_1.2.3              Biobase_2.32.0                          GenomicRanges_1.24.2                    GenomeInfoDb_1.8.3
[11] IRanges_2.6.1                           S4Vectors_0.10.2                        BiocGenerics_0.18.0

loaded via a namespace (and not attached):
[1] edgeR_3.14.0            XVector_0.12.1          zlibbioc_1.18.0         GenomicAlignments_1.8.4 BiocParallel_1.6.3      BSgenome_1.40.1         lattice_0.20-33         tools_3.3.1
[9] grid_3.3.1              rhdf5_2.16.0            csaw_1.6.1              DBI_0.4-1               Rhtslib_1.4.3           Matrix_1.2-6            rtracklayer_1.32.2      bitops_1.0-6
[17] biomaRt_2.28.0          RCurl_1.95-4.8          RSQLite_1.0.0           limma_3.28.17           Rsamtools_1.24.0        Biostrings_2.40.2       locfit_1.5-9.1          XML_3.98-1.4

Would you please help me resolve this?

error • 1.4k views

ADD COMMENT • link 8.2 years ago manjulathimma • 0

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If you don't tag this with diffHic, I won't get notified of your post.

ADD REPLY • link 8.2 years ago Aaron Lun ★ 28k

score 1 · Answer 1 · 2016-09-20

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Aaron Lun ★ 28k

@alun

Last seen 13 hours ago

The city by the bay

See C: diffHic:Fails to load bam file during preparePairs. Don't double-post in two locations, it's annoying.

ADD COMMENT • link 8.2 years ago Aaron Lun ★ 28k

score 0 · Answer 2 · 2016-09-20

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manjulathimma • 0

@manjulathimma-11250

Last seen 8.1 years ago

Hi Aaron,

Removing unwanted chromosome was already done.

frags <- frags[seqnames(frags) %in% paste0("chr",c(1:22,"X","Y"))]
hs.param <- reform(hs.param,fragments=frags)
#Ago1 <- preparePairs("/Users/thimmamp/temp_tobe_deleted/HiCMapped/Ago1_presplitmap_out_fixmate_nochrM.bam",hs.param,file="/Users/thimmamp/temp_tobe_deleted/HiCMapped/Ago1_diffhic.h5",dedup=TRUE,minq=10)
Ago1 <- preparePairs("/Users/thimmamp/temp_tobe_deleted/HiCMapped/Ago1_presplit_out_fixmate_nochrM_new.bam",hs.param,file="/Users/thimmamp/temp_tobe_deleted/HiCMapped/Ago1_diffhic.h5",dedup=TRUE,minq=10)
HepG2 <- preparePairs("/Users/thimmamp/temp_tobe_deleted/HiCMapped/HepG2_presplit_out_fixmate_nochrM_new.bam",hs.param,file="/Users/thimmamp/temp_tobe_deleted/HiCMapped/HepG2_diffhic.h5",dedup=TRUE,minq=10)

I do not understand the need to do it again....

If I should redo this, how would I do it for 'input' object before invoking connectCounts?

ADD COMMENT • link 8.2 years ago manjulathimma • 0

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BTW sorry for double posting!

ADD REPLY • link 8.2 years ago manjulathimma • 0

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No, the error in connectCounts is caused by the fact that you've got chromosomes in regions that aren't in fragments. This requires removing the excess chromosomes from regions. In the code above, you're only removing entries in fragments with chromosomes that aren't in the BAM file, which is a completely different problem.

P.S. Post replies to answers as comments rather than as answers, unless you're actually answering the original post.

ADD REPLY • link 8.2 years ago Aaron Lun ★ 28k

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So How to identify and remove chromosomes in regions that arent in fragments?

ADD REPLY • link 8.2 years ago manjulathimma • 0

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Well, it's pretty simple. Try:

regions[seqnames(regions) %in% seqlevels(frags)]

... or something like that.

ADD REPLY • link 8.2 years ago Aaron Lun ★ 28k

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Sorry for being naive, since I am new to this HiC world!

When I run the command,

regions[seqnames(regions) %in% seqlevels(frags)]
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘seqnames’ for signature ‘"standardGeneric"’

I am following your user guide and at sections 3.2.2 and 3.3

Could you please tell which object should I modify, in order to get rid of unwanted chromosome(s) in the regions file?

ADD REPLY • link 8.2 years ago manjulathimma • 0

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regions is a placeholder for your actual GRanges object. In your case, it is gene.body.

ADD REPLY • link 8.2 years ago Aaron Lun ★ 28k

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I did try to filter unwanted chromosomes,

> gene.body <- gene.body[seqnames(gene.body) %in% seqlevels(frags)]
> redata <- connectCounts(input, hs.param, regions=gene.body)
Error in connectCounts(input, hs.param, regions = gene.body) :
chromosome present in regions and not in fragments
In addition: Warning message:
In connectCounts(input, hs.param, regions = gene.body) :
stranded region ranges have no interpretation, coercing unstrandedness

Why this error is thrown again? Have I done it the right way?

ADD REPLY • link 8.2 years ago manjulathimma • 0

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frags should be the same as whatever hs.param$fragments is. You might also have to try:

gene.body <- gene.body[seqnames(gene.body) %in% 
    seqlevelsInUse(hs.param$fragments)]

This removes the entries in gene.body located on chromosomes that do not exist in hs.param$fragments. If it still doesn't work, help me out and try to diagnose the problem on your end; what chromosomes are present in seqnames(gene.body) that are not present in seqnames(hs.param$fragments)?

ADD REPLY • link 8.2 years ago Aaron Lun ★ 28k

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Hi Aaron,

Thanks for your reply. It is working but with a warning message.

> gene.body <- gene.body[seqnames(gene.body) %in%
+ seqlevelsInUse(hs.param$fragments)]
> redata <- connectCounts(input, hs.param, regions=gene.body)
Warning message:
In connectCounts(input, hs.param, regions = gene.body) :
stranded region ranges have no interpretation, coercing unstrandedness

Can I ignore this warning?

ADD REPLY • link 8.2 years ago manjulathimma • 0

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Yes. It just means that the strandedness of the entries in gene.body are ignored. This is sensible given that Hi-C works on the DNA and doesn't care about the direction of transcription.