Dear All
I'm trying to access columns from the CollapsedVCF object generated by VariantAnnotation::readVcf. I have data for 3847 SNPs in the object, but when sub-setting I get 2 additional entries which I don't know where they come from. Looking at the CollapsedVCF object I can see that there seems to be inconsistency in the length listData (see below).
Help would be much appreciated!
cheers, Fabian
> dim(my_vcf)
[1] 3847 190
> dim(info(my_vcf))
[1] 3847 20
> length(unlist(info(my_vcf)$AF))
[1] 3849
str(info(my_vcf))
Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
..@ rownames : NULL
..@ nrows : int 3847
..@ listData :List of 20
.. ..$ AC :Formal class 'CompressedIntegerList' [package "IRanges"] with 5 slots
.. .. .. ..@ elementType : chr "integer"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
.. .. .. .. .. ..@ end : int [1:3847] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ unlistData : int [1:3849] 234 27 15 195 96 89 121 79 6 3 ...
.. ..$ AF :Formal class 'CompressedNumericList' [package "IRanges"] with 5 slots
.. .. .. ..@ elementType : chr "numeric"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
.. .. .. .. .. ..@ end : int [1:3847] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ unlistData : num [1:3849] 0.616 0.082 0.04 0.595 0.471 ...
.. ..$ AN : int [1:3847] 380 330 374 328 204 200 140 314 348 324 ...
.. ..$ BaseQRankSum : num [1:3847] 0.337 0.715 0.361 0 0 0.727 -0.684 0.55 0.054 0.406 ...
.. ..$ ClippingRankSum: num [1:3847] 0.06 -0.528 0.358 0.278 0.358 0.72 0.48 0.322 0.369 0.736 ...
.. ..$ DP : int [1:3847] 3962 5270 1444 958 342 321 249 609 4623 2274 ...
.. ..$ DS : logi [1:3847] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. ..$ END : int [1:3847] NA NA NA NA NA NA NA NA NA NA ...
.. ..$ ExcessHet : num [1:3847] 9.3468 2.9037 4.4809 0.0002 0 ...
.. ..$ FS : num [1:3847] 0 2.51 3.32 0 6.41 ...
.. ..$ HaplotypeScore : num [1:3847] NA NA NA NA NA NA NA NA NA NA ...
.. ..$ InbreedingCoeff: num [1:3847] -0.0929 -0.0686 -0.0657 0.205 0.3577 ...
.. ..$ MLEAC :Formal class 'CompressedIntegerList' [package "IRanges"] with 5 slots
.. .. .. ..@ elementType : chr "integer"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
.. .. .. .. .. ..@ end : int [1:3847] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ unlistData : int [1:3849] 234 29 16 209 108 105 122 88 6 3 ...
.. ..$ MLEAF :Formal class 'CompressedNumericList' [package "IRanges"] with 5 slots
.. .. .. ..@ elementType : chr "numeric"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
.. .. .. .. .. ..@ end : int [1:3847] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ unlistData : num [1:3849] 0.616 0.088 0.043 0.637 0.529 ...
.. ..$ MQ : num [1:3847] 60 60 60 59.5 55.1 ...
.. ..$ MQRankSum : num [1:3847] -0.025 -0.082 0 0.421 0.358 0.358 0.48 0.55 0.406 -0.718 ...
.. ..$ QD : num [1:3847] 18.3 21.4 15 25.7 28.1 ...
.. ..$ RAW_MQ : num [1:3847] NA NA NA NA NA NA NA NA NA NA ...
.. ..$ ReadPosRankSum : num [1:3847] 0.127 0.736 0.406 0 0.736 0.358 0.736 0.55 -0.553 -0.042 ...
.. ..$ SOR : num [1:3847] 0.669 0.663 0.87 0.632 0.306 0.768 0.916 0.563 0.564 1.19 ...
..@ elementType : chr "ANY"
..@ elementMetadata: NULL
..@ metadata : list()
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] C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] lme4_1.1-12 snpStats_1.22.0
[3] Matrix_1.2-6 survival_2.39-5
[5] VariantAnnotation_1.18.7 Rsamtools_1.24.0
[7] Biostrings_2.40.2 XVector_0.12.1
[9] SummarizedExperiment_1.2.3 Biobase_2.32.0
[11] GenomicRanges_1.24.2 GenomeInfoDb_1.8.3
[13] IRanges_2.6.1 S4Vectors_0.10.2
[15] BiocGenerics_0.18.0 Ssa.RefSeq.db_1.2
[17] RSQLite_1.0.0 DBI_0.4-1
[19] limma_3.28.17 dplyr_0.5.0
[21] plyr_1.8.4 openxlsx_3.0.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.6 nloptr_1.0.4 compiler_3.3.1
[4] GenomicFeatures_1.24.5 bitops_1.0-6 tools_3.3.1
[7] zlibbioc_1.18.0 biomaRt_2.28.0 nlme_3.1-128
[10] tibble_1.1 BSgenome_1.40.1 lattice_0.20-33
[13] rtracklayer_1.32.2 grid_3.3.1 R6_2.1.2
[16] AnnotationDbi_1.34.4 XML_3.98-1.4 BiocParallel_1.6.3
[19] minqa_1.2.4 magrittr_1.5 MASS_7.3-45
[22] GenomicAlignments_1.8.4 splines_3.3.1 assertthat_0.1
[25] RCurl_1.95-4.8 lazyeval_0.2.0
