GOTHiC seqlevel bug
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bef22 • 0
@bef22-7684
Last seen 6.5 years ago
United Kingdom

Hi,

I found a bug in the GOTHiC package. The bug occurs when different seqlevels are present in the read-pairs - even though when making both seqlevels the same.

Please find below a short example of the error.

Best wishes,

Bettina

library(GOTHiC)
library(BSgenome.Dmelanogaster.UCSC.dm3)

# create GRanges object

> sampleName <- "Test"
> paired_reads_1 <- GRanges(seqnames = Rle(c("chr2L", "chr3R", "chrX")),
+                           ranges = IRanges(c(2000, 2000, 2000), c(2100, 2100, 2100)),
+                           strand = c("+", "-", "+"))
> seqlevels(paired_reads_1) <- seqlevels(BSgenome.Dmelanogaster.UCSC.dm3)
> paired_reads_2 <- GRanges(seqnames = Rle(c("chr2L", "chrX", "chrX")),
+                           ranges = IRanges(c(3000, 3000, 3000), c(3100, 3100, 3100)),
+                           strand = c("+", "-", "+"))
> seqlevels(paired_reads_2) <- seqlevels(BSgenome.Dmelanogaster.UCSC.dm3)
> filtered <- GRangesList("paired_reads_1" = paired_reads_1, "paired_reads_2" = paired_reads_2)
> outputfilename <- paste(sampleName, "paired_filtered", sep = "_")
> save(filtered, file = outputfilename)

 

# map reads to fragments

> mapped <- mapReadsToRestrictionSites(filtered,
+                                      sampleName=sampleName,
+                                      BSgenomeName="BSgenome.Dmelanogaster.UCSC.dm3",
+                                      genome=BSgenome.Dmelanogaster.UCSC.dm3,
+                                      restrictionSite="^GATC",
+                                      enzyme="DpnII",
+                                      parallel=FALSE,
+                                      cores=1)

# run GOTHiC

> binom <- GOTHiC(fileName1, fileName2,
+                 sampleName=sampleName,
+                 res=10000,
+                 BSgenomeName="BSgenome.Dmelanogaster.UCSC.dm3",
+                 genome=BSgenome.Dmelanogaster.UCSC.dm3,
+                 restrictionSite="^GATC",
+                 enzyme="DpnII",
+                 cistrans='all',
+                 filterdist=10000,
+                 DUPLICATETHRESHOLD=1,
+                 fileType='BAM', parallel=FALSE, cores=NULL)
Loading paired reads file ...
Loading mapped reads file ...
Computing binomial ...
Error in as.vector(ifelse(df_filtered$chr1 == df_filtered$chr2, abs(df_filtered$locus1 -  :
  error in evaluating the argument 'x' in selecting a method for function 'as.vector': Error in ifelse(df_filtered$chr1 == df_filtered$chr2, abs(df_filtered$locus1 -  :
  error in evaluating the argument 'test' in selecting a method for function 'ifelse': Error in Ops.factor(df_filtered$chr1, df_filtered$chr2) :
  level sets of factors are different

> traceback()
3: as.vector(ifelse(df_filtered$chr1 == df_filtered$chr2, abs(df_filtered$locus1 -
       df_filtered$locus2), Inf))
2: .binomialHiC(interactions, res, sampleName, BSgenomeName, genome,
       restrictionSite, enzyme, parallel, cores, cistrans = cistrans,
       filterdist = filterdist)
1: GOTHiC(fileName1, fileName2, sampleName = sampleName, res = 10000,
       BSgenomeName = "BSgenome.Dmelanogaster.UCSC.dm3", genome = BSgenome.Dmelanogaster.UCSC.dm3,
       restrictionSite = "^GATC", enzyme = "DpnII", cistrans = "all",
       filterdist = 10000, DUPLICATETHRESHOLD = 1, fileType = "BAM",
       parallel = FALSE, cores = NULL)
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 7 (wheezy)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] BSgenome.Dmelanogaster.UCSC.dm3_1.4.0 GOTHiC_1.4.0
 [3] data.table_1.9.4                      BSgenome_1.36.0
 [5] rtracklayer_1.28.2                    Biostrings_2.36.0
 [7] XVector_0.8.0                         GenomicRanges_1.20.3
 [9] GenomeInfoDb_1.4.0                    IRanges_2.2.1
[11] S4Vectors_0.6.0                       BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.5             RColorBrewer_1.1-2      futile.logger_1.4.1
 [4] plyr_1.8.2              bitops_1.0-6            futile.options_1.0.0
 [7] tools_3.2.0             zlibbioc_1.14.0         digest_0.6.8
[10] gtable_0.1.2            lattice_0.20-31         proto_0.3-10
[13] stringr_0.6.2           hwriter_1.3.2           grid_3.2.0
[16] Biobase_2.28.0          XML_3.98-1.1            BiocParallel_1.2.0
[19] latticeExtra_0.6-26     reshape2_1.4.1          ggplot2_1.0.1
[22] lambda.r_1.1.7          Rsamtools_1.20.1        scales_0.2.4
[25] GenomicAlignments_1.4.1 MASS_7.3-40             ShortRead_1.26.0
[28] colorspace_1.2-6        RCurl_1.95-4.6          munsell_0.4.2
[31] chron_2.3-45

 

GOTHiC software error • 714 views
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