Description Usage Arguments Details Value Author(s)
View source: R/breakpoint.finder.interactive.R
Interactive tool to fine tune breakpoint location from the BAM files. An interactive Shiny app will open in your web browser. There, the bp coverage of the 'test.sample' will be shown along with the coverage of the reference samples ('ref.samples'). The user can then slide the breakpoint where the tested samples starts to deviate from the reference. If the deviation is not clear a few parameters (e.g. mapping quality, resolution) can be changed live. Once satisfied the user pushes a button and the function returns the new breakpoint locations. In practice this function can be looped over to quickly fine-tune the breakpoints of several CNVs.
1 2 3 | breakpoint.finder.interactive(chr, start, end, test.sample, files.df,
ref.samples, proper = TRUE, nb.cores = 1, bp.res = 1, flanks = 2000,
related.samples = NULL)
|
chr |
the chromosome |
start |
the start position |
end |
the end position |
test.sample |
the sample with abnormal coverage |
files.df |
a data.frame with the path to the bam files |
ref.samples |
other samples to visualize |
proper |
should proper mapping be counted. |
nb.cores |
number of cores |
bp.res |
default resolution (bp) |
flanks |
default flank size (bp) |
related.samples |
samples related to the 'test.sample' (e.g. parents) to be drawn in a special color. |
Access to the BAM files is necessary, but also to a web-browser (for the application). Hence I would recommend to mount the cluster/server with the BAM on your personnal laptop to use this. Then you might need to tweak a bit the paths in the 'bam' column of 'files.df' to include your mounting location.
a list with
bk.df |
a data.frame with the breakpoint coordinates |
graph |
the ggplot object with the final graph |
Jean Monlong
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