Question: An error while finding pintersect()
gravatar for Prashantha Hebbar
21 days ago by
Prashantha Hebbar260 wrote:

Dear all, I have to find percentage of overlap between two genomic range objects (reference and test) and get those coordinates having more than 50% overlap in test genomic range object. I have tried scripts available in forum, but while running pintersect() function i find below error. would you please suggest me how to solve below error?

Error in seqinfo<-(*tmp*, value = <s4 object="" of="" class="" "seqinfo"="">) : could not find symbol "force" in environment of the generic function

Regards, Prashantha

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REF = structure(list(chr = c("1", "1", "1", "1", "1", "1", "1", "1", + "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1"), + start = c(766101L, 1627918L, 4421060L, 7324468L, 8053732L, + 8182462L, 8182584L, 8182584L, 8206130L, 8804237L, 10369546L, + 10370541L, 10543836L, 10656324L, 12354307L, 12841928L, 12845863L, + 12909237L, 12909965L, 13444908L), end = c(809773L, 1672603L, + 4424115L, 7325408L, 8067990L, 8189854L, 8189285L, 8189285L, + 8209321L, 8812660L, 10377983L, 10377983L, 10545046L, 10657912L, + 12357076L, 12971833L, 12883096L, 12927107L, 12918079L, 13468022L + ), Deft = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1)), .Names = c("chr", "start", "end", "Deft" + ), row.names = c(217L, 568L, 1340L, 1691L, 1804L, 1811L, 1812L, + 1813L, 1819L, 1880L, 2017L, 2020L, 2041L, 2049L, 2224L, 2282L, + 2284L, 2332L, 2335L, 2424L), class = "data.frame")

TEST = structure(list(sampleID = c("SID1331", "SID1331", "SID1331", + "SID1331", "SID1331", "SID1331", "SID1331", "SID1331", "SID1331", + "SID1331", "SID1337", "SID1337", "SID1337", "SID1337", "SID1337", + "SID1337", "SID1337", "SID1337", "SID1337", "SID1337", "SID1337" + ), Chromosome = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 10L, + 10L, 11L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L), Start = c(61735L, + 7541291L, 32664866L, 45935056L, 55449273L, 117769301L, 117892183L, + 167580307L, 172458743L, 172852403L, 129495492L, 129526092L, 198572L, + 112837740L, 112847206L, 132105712L, 132126171L, 150442L, 23261653L, + 23270278L, 28135989L), End = c(7539746L, 32664843L, 45934562L, + 55445562L, 117767918L, 117886211L, 167580003L, 172457651L, 172851634L, + 214938359L, 129525791L, 135506704L, 112837593L, 112846803L, 132104437L, + 132122974L, 134944770L, 23261612L, 23268885L, 28131521L, 52920414L + )), .Names = c("sampleID", "Chromosome", "Start", "End"), row.names = c(1L, + 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 1000L, 1001L, 1002L, 1003L, + 1004L, 1005L, 1006L, 1007L, 1008L, 1009L, 1010L), class = "data.frame") library(GenomicRanges) Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append,, cbind, colnames,,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
paste, pmax,, pmin,, Position, rank, rbind,
Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges Loading required package: GenomeInfoDb

refGR <- makeGRangesFromDataFrame(REF) testGR <- makeGRangesFromDataFrame(TEST) hits <- findOverlaps(refGR, testGR) overlaps <- pintersect(refGR[queryHits(hits)], testGR[subjectHits(hits)]) Error in seqinfo<-(*tmp*, value = <s4 object="" of="" class="" "seqinfo"="">) : could not find symbol "force" in environment of the generic function sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 17.10

Matrix products: default BLAS: /usr/lib/x8664-linux-gnu/openblas/ LAPACK: /usr/lib/x8664-linux-gnu/

[3] LC
[5] LC
[7] LC

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] GenomicRanges1.26.4 GenomeInfoDb1.14.0 IRanges2.8.2
[4] S4Vectors
0.12.2 BiocGenerics_0.20.0

loaded via a namespace (and not attached): [1] zlibbioc1.24.0 compiler3.4.2 XVector0.14.1
[4] GenomeInfoDbData
1.0.0 RCurl1.95-4.12 bitops1.0-6

genomicranges • 94 views
ADD COMMENTlink written 21 days ago by Prashantha Hebbar260

Your version of R/Bioconductor is a few years old and no longer supported. Please update and see if the problem persists.

ADD REPLYlink written 21 days ago by Michael Lawrence11k
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