Entering edit mode
I think this commit:
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r73720 | hpages@fhcrc.org | 2013-02-24 23:17:38 -0800 (Sun, 24 Feb
2013) |
3 lines
Tweak to GRanges() constructor so the names of the supplied metadata
cols
don't
run in conflict with some obscure internal argument names.
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Means that we can no longer do this:
mycol <- 1
GRanges("chr1", IRanges(1, 10), "+", mycol)
And get a GRanges with a metadata column named "mycol" like we get
with
DataFrame and data.frame. This is a pretty big change in behavior that
is
breaking code.
In other words, we now get this:
GRanges with 1 range and 1 metadata column:
seqnames ranges strand | *1*
<rle> <iranges> <rle> | <numeric>
[1] chr1 [1, 10] + | 1
---
seqlengths:
chr1
NA
While I'm pretty sure we used to get:
GRanges with 1 range and 1 metadata column:
seqnames ranges strand | *mycol*
<rle> <iranges> <rle> | <numeric>
[1] chr1 [1, 10] + | 1
---
seqlengths:
chr1
NA
Michael
R Under development (unstable) (2013-03-27 r62427)
Platform: x86_64-unknown-linux-gnu (64-bit)
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=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] tools parallel stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] isoseq_0.0.8 Rsamtools_1.11.27
[3] Biostrings_2.27.13 org.Hs.eg.db_2.9.0
[5] RSQLite_0.11.2 DBI_0.2-5
[7] TxDb.Hsapiens.BioMart.igis_2.1.2 GenomicFeatures_1.11.16
[9] AnnotationDbi_1.21.16 Biobase_2.19.3
[11] GenomicRanges_1.11.42 IRanges_1.17.41
[13] BiocGenerics_0.5.6 CGPtools_2.0.54
loaded via a namespace (and not attached):
[1] annotate_1.37.4 biomaRt_2.15.1
biovizBase_1.7.8
[4] bitops_1.0-5 BSgenome_1.27.1
cluster_1.14.4
[7] colorspace_1.2-1 DESeq_1.11.6
dichromat_2.0-0
[10] digest_0.6.3 genefilter_1.41.4
geneplotter_1.37.0
[13] ggbio_1.7.14 ggplot2_0.9.3.1
grid_3.1.0
[16] gridExtra_0.9.1 gtable_0.1.2
Hmisc_3.10-1
[19] labeling_0.1 lattice_0.20-15
MASS_7.3-26
[22] Matrix_1.0-12 munsell_0.4
plyr_1.8
[25] proto_0.3-10 RColorBrewer_1.0-5
RCurl_1.95-4.1
[28] reshape2_1.2.2 rjson_0.2.12
rtracklayer_1.19.11
[31] scales_0.2.3 splines_3.1.0
stats4_3.1.0
[34] stringr_0.6.2 survival_2.37-4
VariantAnnotation_1.5.45
[37] XML_3.96-0.2 xtable_1.7-1
zlibbioc_1.5.0
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