imputeBsDifferencesForTestdata: Impute artificial differences in the example data set

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

Impute artificial differences in the example data set

Description

A function that works only on the test data set provided with the package. It is used for internal testing and the making of examples to showcase the differential binding functions.

Usage

imputeBsDifferencesForTestdata(object, size = 5, change.per = 0.1)

Arguments

object	a BSFDataSet object; explicitly the test data set from the extdata folder
size	numeric; the number of positions on which signal should be deleted, counting from the start
change.per	numeric; the percentage of ranges that should be effected by the change.

Details

Differences between samples are artificially introduced by removing the signal on a random set of binding sites of the input.

Value

object a BSFDataSet object with the signal slot adapted to reflect changes in binding between two artificial conditions

Examples

# load clip data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))
load(list.files(files, pattern = ".rds$", full.names = TRUE)[1])

bds = makeBindingSites(bds, bsSize = 7)
bds = assignToGenes(bds, anno.genes = gns)

bds = imputeBsDifferencesForTestdata(bds)

ZarnackGroup/BindingSiteFinder documentation built on Nov. 24, 2024, 10:41 a.m.