calculateBsBackground: Compute background coverage for binding sites per gene

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

Compute background coverage for binding sites per gene

Description

This function computes the background coverage used for the differential binding analysis to correct for transcript level changes. Essentially, the crosslink signal on each gene is split into crosslinks that can be attributed to the binding sites and all other signal that can be attributed to the background.

Usage

calculateBsBackground(
  object,
  anno.annoDB = NULL,
  anno.genes = NULL,
  blacklist = NULL,
  use.offset = TRUE,
  ranges.offset = NULL,
  match.geneID.gene = "gene_id",
  match.geneID.bs = "geneID",
  match.geneID.blacklist = "geneID",
  generate.geneID.bs = FALSE,
  generate.geneID.blacklist = FALSE,
  uniqueID.gene = "gene_id",
  uniqueID.bs = "bsID",
  uniqueID.blacklist = "bsID",
  force.unequalSites = FALSE,
  quiet = FALSE,
  veryQuiet = TRUE,
  ...
)

Arguments

object	a BSFDataSet object with two conditions
anno.annoDB	an object of class OrganismDbi that contains the gene annotation.
anno.genes	an object of class GenomicRanges that represents the gene ranges directly
blacklist	GRanges; genomic ranges where the signal should be excluded from the background
use.offset	logical; if an offset region around the binding sites should be used on which the signal is excluded from the background
ranges.offset	numeric; number of nucleotides the offset window around each binding site should be wide (defaults to 1/2 binding site width - NULL)
match.geneID.gene	character; the name of the column with the gene ID in the genes meta columns used for matching binding sites to genes
match.geneID.bs	character; the name of the column with the gene ID in the binding sites meta columns used for matching binding sites to genes
match.geneID.blacklist	character; the name of the column with the gene ID in the blacklist meta columns used for matching the blacklist regions with the genes
generate.geneID.bs	logical; if the binding site to gene matching should be performed if no matching gene ID is provided
generate.geneID.blacklist	logical; if the blacklist to gene matching should be performed if no matching gene ID is provided
uniqueID.gene	character; column name of a unique ID for all genes
uniqueID.bs	character; column name of a unique ID for all binding sites
uniqueID.blacklist	character; column name of a unique ID for all blacklist regions
force.unequalSites	logical; if binding sites of not identical width should be allowed or not
quiet	logical; whether to print messages or not
veryQuiet	logical; whether to print messages or not
...	additional arguments; passed to assignToGenes

Details

To avoid that crosslinks from binding sites contaminate the background counts a protective region around each binding sites can be spanned with use.offset the default width of the offset region is half of the binding site width, but can also be changed with the ranges.offset parameter.

Additional region that one wants to exclude from contributing to the background signal can be incorporated as GRanges objects through the blacklist option.

It is expected that binding sites are assigned to hosting genes prior to running this funciton (see BSFind). This means a unique gene ID is present in the meta columns of each binding site ranges. If this is not the case one can invoce the binding site to gene assignment with generate.geneID.bs. The same is true for the blacklist regions with option generate.geneID.blacklist.

It is expected that all binding sites are of the same size (See BSFind on how to achieve this). If this is however not the case and one wants to keep binding sites of different with then option force.unequalSites can be used.

This function is intended to be used for the generation of the count matrix used for the differential binding analysis. It is usually preceded by combineBSF and followed by filterBsBackground.

Value

an object of class BSFDataSet with counts for binding sites, background and total gene added to the meta column of the ranges

See Also

combineBSF, filterBsBackground

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])

# make binding sites
bds = makeBindingSites(bds, bsSize = 7)
bds = assignToGenes(bds, anno.genes = gns)

# change meta data
m = getMeta(bds)
m$condition = factor(c("WT", "WT", "KO", "KO"), levels = c("WT", "KO"))
bds = setMeta(bds, m)

# change signal
s = getSignal(bds)
names(s$signalPlus) = paste0(m$id, "_", m$condition)
names(s$signalMinus) = paste0(m$id, "_", m$condition)
bds = setSignal(bds, s)

# make example blacklist region
myBlacklist = getRanges(bds)
set.seed(1234)
myBlacklist = sample(myBlacklist, size = 500) + 4

# make background
bds.b1 = calculateBsBackground(bds, anno.genes = gns)

# make background - no offset
bds.b2 = calculateBsBackground(bds, anno.genes = gns, use.offset = FALSE)

# make background - use blacklist
bds.b3 = calculateBsBackground(bds, anno.genes = gns, blacklist = myBlacklist)

ZarnackGroup/BindingSiteFinder documentation built on May 31, 2024, 3:29 a.m.