Hi,
I was able to run FourCSeq successfully till I hit the following error:
> getZScores(fcAce)
[1] "viewpoint_1"
Error in object[seqnames(object) == unique(colData(object)$chr), ] :
error in evaluating the argument 'i' in selecting a method for function '[': Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "S4Vectors") :
Rle of type 'list' is not supported
Here's what I ran before getZScores():
>library(FourCSeq)
>exptDataAce=SimpleList(projectPath=getwd(), fragmentDir='bams/', referenceGenomeFile='/home/user/ref/mm9/bt2/chr_fa/chr7.fa', reSequence1='GATC', reSequence2='GTAC', primerFile='Primers.fa', bamFilePath='bams/')
>colDataAce=DataFrame(viewpoint="viewpoint_1", condition=factor(c("WT","WT","KO","KO")),levels = c("WT1","WT2","KO1","KO2"), replicate = c(1,2,1,2), bamFile = c('wt1.bam','wt2.bam','ko1.bam','ko2.bam'), sequencingPrimer="first")
>fcAce=FourC(colDataAce,exptDataAce)
>fcAce=addFragments(fcAce,save=TRUE)
>findViewpointFragments(fcAce)
>load('bams/primerFragments.rda')
>colData(fcAce)$chr = vpFrag[2]
>colData(fcAce)$start = vpFrag[3]
>colData(fcAce)$end = vpFrag[4]
>fcAce=countFragmentOverlaps(fcAce, trim=4)
>fcAce=combineFragEnds(fcAce)
>writeTrackFiles(fcAce)
>fcAceZ=getZScores(fcAce)
The error is probably coming from :
object <- object[seqnames(object) == unique(colData(object)$chr),]
of FourCSeq/R/functions.R (line 418).
Running this :
seqnames(fcAce) == unique(colData(fcAce)$chr)
produces the error : Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "S4Vectors") :
Rle of type 'list' is not supported
> seqnames(fcAce)
factor-Rle of length 160846 with 1 run
Lengths: 160846
Values : chr7
Levels(1): chr7
AND
> unique(colData(fcAce)$chr)
[[1]]
[1] chr7
Levels: chr7
are the input objects. It appears that all of our elements in seqnames(fcAce) are ALREADY limited to chr7 because of how we aligned.
Upon searching I also found similar errors thrown by some other packages. Is there another method called by getZScores() which is incompatible with RleList object? Any suggestions/fixes will be much appreciated.
Thanks,
Maddie
P.S. R sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] FourCSeq_1.2.0 LSD_3.0
[3] DESeq2_1.8.2 RcppArmadillo_0.6.500.4.0
[5] Rcpp_0.12.3 ggplot2_2.1.0
[7] GenomicRanges_1.20.8 GenomeInfoDb_1.4.3
[9] IRanges_2.2.9 S4Vectors_0.6.6
[11] BiocGenerics_0.14.0
loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 biovizBase_1.16.0
[3] lattice_0.20-33 gtools_3.5.0
[5] Rsamtools_1.20.5 Biostrings_2.36.4
[7] plyr_1.8.3 futile.options_1.0.0
[9] acepack_1.3-3.3 RSQLite_1.0.0
[11] zlibbioc_1.14.0 GenomicFeatures_1.20.6
[13] annotate_1.46.1 rpart_4.1-10
[15] Matrix_1.2-4 ggbio_1.16.1
[17] BiocParallel_1.2.22 geneplotter_1.46.0
[19] stringr_1.0.0 foreign_0.8-66
[21] RCurl_1.95-4.8 biomaRt_2.24.1
[23] munsell_0.4.3 rtracklayer_1.28.10
[25] nnet_7.3-12 gridExtra_2.2.1
[27] Hmisc_3.17-2 XML_3.98-1.4
[29] reshape_0.8.5 GenomicAlignments_1.4.2
[31] bitops_1.0-6 RBGL_1.44.0
[33] grid_3.2.2 xtable_1.8-2
[35] GGally_1.0.1 gtable_0.2.0
[37] DBI_0.3.1 magrittr_1.5
[39] scales_0.4.0 graph_1.46.0
[41] stringi_1.0-1 XVector_0.8.0
[43] reshape2_1.4.1 genefilter_1.50.0
[45] latticeExtra_0.6-28 futile.logger_1.4.1
[47] Formula_1.2-1 lambda.r_1.1.7
[49] RColorBrewer_1.1-2 tools_3.2.2
[51] dichromat_2.0-0 BSgenome_1.36.3
[53] Biobase_2.28.0 OrganismDbi_1.10.0
[55] survival_2.38-3 AnnotationDbi_1.30.1
[57] colorspace_1.2-6 cluster_2.0.3
[59] fda_2.4.4 VariantAnnotation_1.14.13
