Description Usage Arguments Details Value Author(s) Examples
This function accepts two or more recoup
output objects holding single samples to a merged object
so that all samples can be used together. This is useful
when many coverages must be calulated/plotted and memory
issues do not allow effective parallelization.
1 2 |
... |
one or more |
withDesign |
one of |
dropPlots |
if profile and/or heatmap plots are
attached to the input object(s), they will be
recalculated if |
.
The withDesign
argument controls what should be
done if any input has an attached design. The default
behavioir ("auto"
) will try to do its best to
preserve compatible designs. If one or more inputs have
the same design, it will be applied to the rest of the
samples. If there is only one design, it will be applied
to all samples (if you don't want this to happen, choose
"drop"
). If more than one sample has an attached
design but these are incompatible (different numbers of
rows/rownames, columns/columnnames), then all designs
are dropped. Obviously, withDesign="drop"
drops
all attached designs and the output object is free of
a design data frame.
A recoup
output object with as many
samples as in ...
.
Panagiotis Moulos
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | # Load some data
data("recoup_test_data",package="recoup")
test.input.shift <- test.input
names(test.input.shift) <- paste(names(test.input.shift),"_1",sep="")
test.input.shift[[1]]$id <- paste0(test.input.shift[[1]]$id,"_1")
test.input.shift[[1]]$ranges <-
shift(test.input.shift[[1]]$ranges,100)
test.input.shift[[2]]$id <- paste0(test.input.shift[[2]]$id,"_1")
test.input.shift[[2]]$ranges <-
shift(test.input.shift[[2]]$ranges,100)
test.tss.1 <- recoup(
test.input,
design=NULL,
region="tss",
type="chipseq",
genome=test.genome,
flank=c(2000,2000),
selector=NULL,
rc=0.1
)
test.tss.2 <- recoup(
test.input.shift,
design=NULL,
region="tss",
type="chipseq",
genome=test.genome,
flank=c(2000,2000),
selector=NULL,
rc=0.1
)
test.tss <- mergeRuns(test.tss.1,test.tss.2)
|
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