collapseBins {chromstaR} | R Documentation |
The function will collapse consecutive bins which have, for example, the same combinatorial state.
collapseBins( data, column2collapseBy = NULL, columns2sumUp = NULL, columns2average = NULL, columns2getMax = NULL, columns2drop = NULL )
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. |
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 |
A data.frame.
Aaron Taudt
## 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)