the minimum score for a structural variation
to be read in.
readsSupport
the minimum read pair support for a
structural variation to be read in.
regSizeLowerCutoff
the minimum size for a structural
variation to be read in.
regSizeUpperCutoff
the maximum size for a structural
variation to be read in.
method
a tag to assign to the result of this function.
...
parameters passed to read.table.
Details
The predicted SVs could be further filtered by score,
number of read pairs supporting the occurence of a specific SV,
and the predicted size of SVs to get more reliable SVs. See our
paper for more details.
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> library(intansv)
Loading required package: plyr
Loading required package: ggbio
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: ggplot2
Need specific help about ggbio? try mailing
the maintainer or visit http://tengfei.github.com/ggbio/
Attaching package: 'ggbio'
The following objects are masked from 'package:ggplot2':
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
xlim
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:plyr':
rename
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:plyr':
desc
Loading required package: GenomeInfoDb
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/intansv/readBreakDancer.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readBreakDancer
> ### Title: Read in the structural variations predicted by breakDancer
> ### Aliases: readBreakDancer
>
> ### ** Examples
>
>
> breakdancer <- readBreakDancer(system.file("extdata/ZS97.breakdancer.sv",
+ package="intansv"))
> str(breakdancer)
List of 2
$ del:'data.frame': 1007 obs. of 4 variables:
..$ chromosome: chr [1:1007] "chr05" "chr05" "chr05" "chr05" ...
..$ pos1 : num [1:1007] 65586 86442 120288 153694 201845 ...
..$ pos2 : num [1:1007] 65938 87430 127670 153801 201959 ...
..$ size : num [1:1007] 353 988 7382 107 114 ...
$ inv:'data.frame': 17 obs. of 4 variables:
..$ chromosome: chr [1:17] "chr05" "chr05" "chr05" "chr05" ...
..$ pos1 : num [1:17] 1291574 6942451 12014581 15092428 18770962 ...
..$ pos2 : num [1:17] 1291678 6944637 12015915 15157500 18771414 ...
..$ size : num [1:17] 105 2186 1334 65072 452 ...
- attr(*, "method")= chr "BreakDancer"
>
>
>
>
>
>
> dev.off()
null device
1
>