Collapse consecutive bins

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Description

The function will collapse consecutive bins which have, for example, the same combinatorial state.

Usage

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collapseBins(data, column2collapseBy = NULL, columns2sumUp = NULL,
  columns2average = NULL, columns2getMax = NULL, columns2drop = NULL)

Arguments

data

A data.frame containing the genomic coordinates in the first three columns.

column2collapseBy

The number of the column which will be used to collapse all other inputs. If a set of consecutive bins has the same value in this column, they will be aggregated into one bin with adjusted genomic coordinates.

columns2sumUp

Column numbers that will be summed during the aggregation process.

columns2average

Column numbers that will be averaged during the aggregation process.

columns2getMax

Column numbers where the maximum will be chosen during the aggregation process.

columns2drop

Column numbers that will be dropped after the aggregation process.

Details

The following tables illustrate the principle of the collapsing:

Input data:

seqnames start end column2collapseBy moreColumns columns2sumUp
chr1 0 199 2 1 10 1 3
chr1 200 399 2 2 11 0 3
chr1 400 599 2 3 12 1 3
chr1 600 799 1 4 13 0 3
chr1 800 999 1 5 14 1 3

Output data:

seqnames start end column2collapseBy moreColumns columns2sumUp
chr1 0 599 2 1 10 2 9
chr1 600 999 1 4 13 1 6

Value

A data.frame.

Author(s)

Aaron Taudt

Examples

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## Load example data
## Get an example multiHMM
file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData",
                    package="chromstaR")
model <- get(load(file))
df <- as.data.frame(model$bins)
shortdf <- collapseBins(df, column2collapseBy='state', columns2sumUp='width', columns2average=6:9)

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