Entering edit mode
12.7 years ago
Jeremy Leipzig
23k
It seems like the casting routine to assign names to GRanges from GappedAlignments is more natural than the GRanges constructor.
library("GenomicRanges")
feature1 <- GRanges(names="feature1",seqnames="chr1", IRanges(start=1, width=100), strand="*")
featureGA <- GappedAlignments(names="feature2", seqnames = Rle("chr1"), pos = as.integer(25),cigar = "100M", strand = strand("*"))
feature2<-as(feature2,"GRanges")
> feature1
GRanges with 1 range and 1 elementMetadata col:
seqnames ranges strand | names
<Rle> <IRanges> <Rle> | <character>
[1] chr1 [1, 100] * | feature1
---
seqlengths:
chr1
NA
> feature2
GRanges with 1 range and 0 elementMetadata cols:
seqnames ranges strand
<Rle> <IRanges> <Rle>
feature2 chr1 [25, 124] *
---
seqlengths:
chr1
NA
both<-GRangesList(features=feature1,feature2=feature2)
Error in .Method(..., deparse.level = deparse.level) :
number of columns for arg 2 do not match those of first arg
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicRanges_1.8.4 IRanges_1.14.2 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] stats4_2.15.0 tools_2.15.0