Regions of high signal in the input samples of a ChIP experiment can lead to artefacts in peak calling. This class generates "grey lists" of such regions, for use in filtering reads before peak calling (or filtering peaks after peak calling, though it is generally safer to filter first).
Objects can be created by calls of the
new("GreyList", genome, ...),
genome is a
"BSgenome" object describing a genome, such as
BSgenome.Hsapiens.UCSC.hg19. Alternatively, a karyotype
file can be provided explictly:
new("GreyList", karyoFile=fn, ...).
karyoFile must be provided; if both are present,
BSgenome object takes precedence. Alternatively,
an explicit list of regions may be provided as a
corresponding with the genome the reads are aligned to
Seqinfo object from
BSgenome object, or made from the
The name of a file containing chromosome sizes for the reference genome of interest, one per line, as "chromName chromLength" pairs.
that defines which regions of the genome should be used to build
the grey list. This is to allow the list to be built on just part
of the genome.
GRanges object with an
overlapping tiling of the genome (by default 1Kb tiles every 512b).
A numeric vector holding the counts corresponding to the tiling and the BAM file provided.
A vector of BAM filenames that were used to generate the counts (currently only accepts one).
The computed estimates of the "size" parameter
of the negative binomial distribution, estimated by
MASS::fitdistr from repeated sampling from the counts.
The standard errors of the "size" parameters, as
The mean of the "size" estimates.
Computed estimates of the "mu" parameter of the
negative binomial distribution, estimated by
from repeated sampling from the counts.
The standard errors of the "mu" parameter.
The mean of the "mu" estimates.
How many samples from the counts were taken.
How many values were sampled from the counts, for each estimate of "size" and "mu".
The requested p-value threshold.
The calculated threshold, based on the p-value.
The largest gap to consider when merging nearby regions (i.e. if there are "grey" regions up to this many nucleotides apart, merge them into one long region).
GRanges object defining the
final grey list regions.
The percentage of the genome covered by the grey list regions.
signature(obj = "GreyList"): Calculate the
cutoff for reads in bins, based on fitting the counts to a negative
signature(obj = "GreyList"): Count reads in bins
across the genome.
signature(object = "GreyList",
con = "character", format = "missing"): Write the grey list
to a file.
signature(.Object = "GreyList"): Create an initial
object (invoked automatically by
signature(obj = "GreyList"): Load a genome
description from a file. The file format is one line per chromosome,
with the name of the chromosome followed by white space followed by
an integer indicating the length of the chromosome.
signature(obj = "GreyList"): Get the karyotype
of a genome from a
signature(obj = "GreyList"): Set the region(s)
of a genome to use in making the
signature(obj = "GreyList"): Compute the actual
grey list, after calculating the threshold.
signature(object = "GreyList"): Display the grey list.
Gord Brown ([email protected])
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