Hi,
I would like to retrieve phastconsscores for a set of ranges from the package 'phastCons100way.UCSC.hg19'. By default, scores will average the retrieved phastconsscores if more than one position is retrieved. Here I retrieve 10 times two positions. Interestingly, I get different values if I retrieve the scores for the entire set of ranges or, respectively, for just a subset:
library(BSgenome.Hsapiens.UCSC.hg19)
library(Genomicanges)
library(phastCons100way.UCSC.hg19)
x = GRanges(seqnames = c("chr12", "chr15", "chr15", "chr2","chr2", "chr2","chr3","chr5","chr2","chr15"),
ranges = IRanges(start = c(46357547, 99482408,99482417,42484368,42484372, 180849279,63983256,38952875, 85768190, 83676233),
width = rep(2,10)), strand = rep("+",10))
scores(phastCons100way.UCSC.hg19, x)
[1] 0.00 0.00 0.00 0.05 0.00 0.00 0.00 0.00 0.00 0.00
scores(phastCons100way.UCSC.hg19, x[1:4])
[1] 0 0 0 0
Why do I have on the fourth position once '0' and once '0.5'?
Best,
Stefanie
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] phastCons100way.UCSC.hg19_3.1.0 VariantFiltering_1.4.0
[3] VariantAnnotation_1.14.0 Rsamtools_1.20.0
[5] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.36.0
[7] rtracklayer_1.28.0 Biostrings_2.36.0
[9] XVector_0.8.0 GenomicRanges_1.20.1
[11] GenomeInfoDb_1.4.0 IRanges_2.2.0
[13] S4Vectors_0.6.0 BiocGenerics_0.14.0
loaded via a namespace (and not attached):
[1] Rcpp_0.11.5 biovizBase_1.16.0 lattice_0.20-31
[4] digest_0.6.8 mime_0.3 R6_2.0.1
[7] plyr_1.8.1 futile.options_1.0.0 acepack_1.3-3.3
[10] RSQLite_1.0.0 ggplot2_1.0.1 zlibbioc_1.14.0
[13] GenomicFeatures_1.20.0 rpart_4.1-9 proto_0.3-10
[16] splines_3.2.0 BiocParallel_1.2.0 stringr_0.6.2
[19] foreign_0.8-63 RCurl_1.95-4.5 biomaRt_2.24.0
[22] munsell_0.4.2 shiny_0.11.1 httpuv_1.3.2
[25] Gviz_1.12.0 htmltools_0.2.6 nnet_7.3-9
[28] Hmisc_3.15-0 matrixStats_0.14.0 XML_3.98-1.1
[31] GenomicAlignments_1.4.0 MASS_7.3-40 bitops_1.0-6
[34] grid_3.2.0 RBGL_1.44.0 xtable_1.7-4
[37] gtable_0.1.2 DBI_0.3.1 scales_0.2.4
[40] graph_1.46.0 reshape2_1.4.1 latticeExtra_0.6-26
[43] futile.logger_1.4 Formula_1.2-1 lambda.r_1.1.7
[46] RColorBrewer_1.1-2 tools_3.2.0 RJSONIO_1.3-0
[49] dichromat_2.0-0 Biobase_2.28.0 survival_2.38-1
[52] AnnotationDbi_1.30.0 colorspace_1.2-6 cluster_2.0.1