combineBSF: Combine multiple 'BSFDataSet' objects

In ZarnackGroup/BindingSiteFinder: Binding site defintion based on iCLIP data

Combine multiple BSFDataSet objects

Description

This function combines all BSFDataSet objects from the input list into a single BSFDataSet object.

Usage

combineBSF(
  list,
  overlaps.fix = TRUE,
  combine.bsSize = NULL,
  combine.name = NULL,
  force.reload = FALSE,
  quiet = TRUE,
  veryQuiet = FALSE
)

Arguments

list	list; a list of objects from class BSFDataSet that should be combined
overlaps.fix	logical; if partially overlapping binding sites should be re-centered
combine.bsSize	numeric; the binding site size that the merged sites should have. Default=NULL, then bsSize is taken from the input objects in list.
combine.name	character; meta table name of the combined object. Default=NULL; then name is set to 'combined'
force.reload	logical; whether the signal should be derived from the merge of the input objects given in list or if the signal should be re-loaded from the path given in the meta data.
quiet	logical; whether to print messages or not
veryQuiet	logical; whether to print status messages or not

Details

Meta-data tables are added to each other by performing a row-wise bind, basically adding all meta data tables underneath each other.

The default way of signal combination is merging all signal lists on the level of the indivdual samples. One can also force a re-load of the signal list component by using force.reload=TRUE. The signal can be combined by

The ranges are combined by adding both granges objects together. With option overlaps.fix one can decide if partially overlapping ranges should be combined into a single range or not. If this option is FALSE one is likely to have overlapping binding sites after the merge. If this option is TRUE, then the combined coverage is used to guide the new center point for these cases.

The combine.bsSize option allows one to set a unique bsSize for all objects that should be combined. Although it is recommended to combine only objects with the same bsSize this option can be used to ensure that the merged result has the same bsSize for all ranges.

This function is usually used to combine two datasets in the context of a differntial testing analysis.

Value

an object of class BSFDataSet with ranges, signal and meta data resulting from the merge of the input objects.

See Also

processingStepsFlowChart, calculateBsBackground

Examples

# load clip data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))

# make binding sites
bds = makeBindingSites(bds, bsSize = 7)

# split ranges in two groups
allRanges = getRanges(bds)
set.seed(1234)
idx = sample(1:length(allRanges), size = length(allRanges)/2, replace = FALSE)
r1 = allRanges[idx]
r2 = allRanges[-idx]

# splite meta data
allMeta = getMeta(bds)
m1 = allMeta[1:2,]
m2 = allMeta[3:4,]

# create new objects
bds1 = setRanges(bds, r1)
bds2 = setRanges(bds, r2)
bds1 = setMeta(bds1, m1)
bds2 = setMeta(bds2, m2)
bds1 = setName(bds1, "test1")
bds2 = setName(bds2, "test2")

# merge two objects with '+' operator
c1 = bds1 + bds2

# merge two objects from list
list = list(bds1, bds2)
c1 = combineBSF(list = list, overlaps.fix = TRUE,
 combine.bsSize = NULL, combine.name = NULL, quiet = TRUE)

ZarnackGroup/BindingSiteFinder documentation built on May 2, 2024, 12:38 a.m.