getGRegionsStat: Statistic of Genomic Regions

In genomaths/MethylIT.utils: MethylIT utility

Statistic of Genomic Regions

Description

A function to estimate summarized measures of a specified variable given in a GRanges object (a column from the metacolums of the GRanges object) after split the GRanges object into intervals. A faster alternative would be getGRegionsStat2.

Usage

getGRegionsStat(
  GR,
  win.size = 1,
  step.size = 1,
  grfeatures = NULL,
  stat = c("sum", "mean", "gmean", "median", "density", "count", "denCount"),
  absolute = FALSE,
  select.strand = NULL,
  column = 1L,
  prob = FALSE,
  entropy = FALSE,
  maxgap = -1L,
  minoverlap = 0L,
  scaling = 1000L,
  logbase = 2,
  missings = 0,
  type = c("within", "any", "start", "end", "equal"),
  ignore.strand = FALSE,
  naming = FALSE,
  col.names = NULL,
  output = c("hits", "all"),
  verbose = TRUE,
  ...
)

## S4 method for signature 'GRanges'
getGRegionsStat(
  GR,
  win.size = 350,
  step.size = 350,
  grfeatures = NULL,
  stat = c("sum", "mean", "gmean", "median", "density", "count", "denCount"),
  absolute = FALSE,
  select.strand = NULL,
  column = 1L,
  prob = FALSE,
  entropy = FALSE,
  maxgap = -1L,
  minoverlap = 0L,
  scaling = 1000L,
  logbase = 2,
  missings = 0,
  type = c("within", "any", "start", "end", "equal"),
  ignore.strand = FALSE,
  naming = FALSE,
  col.names = NULL,
  output = c("hits", "all")
)

## S4 method for signature 'list'
getGRegionsStat(
  GR,
  win.size = 350,
  step.size = 350,
  grfeatures = NULL,
  stat = c("sum", "mean", "gmean", "median", "density", "count", "denCount"),
  absolute = FALSE,
  select.strand = NULL,
  column = 1L,
  prob = FALSE,
  entropy = FALSE,
  maxgap = -1L,
  minoverlap = 0L,
  scaling = 1000L,
  logbase = 2,
  missings = 0,
  type = c("within", "any", "start", "end", "equal"),
  ignore.strand = FALSE,
  naming = FALSE,
  col.names = NULL,
  output = c("hits", "all"),
  num.cores = 1L,
  tasks = 0,
  verbose = TRUE,
  ...
)

## S4 method for signature 'InfDiv'
getGRegionsStat(
  GR,
  win.size = 350,
  step.size = 350,
  grfeatures = NULL,
  stat = c("sum", "mean", "gmean", "median", "density", "count", "denCount"),
  absolute = FALSE,
  select.strand = NULL,
  column = 1L,
  prob = FALSE,
  entropy = FALSE,
  maxgap = -1L,
  minoverlap = 0L,
  scaling = 1000L,
  logbase = 2,
  missings = 0,
  type = c("within", "any", "start", "end", "equal"),
  ignore.strand = FALSE,
  naming = FALSE,
  col.names = NULL,
  output = c("hits", "all"),
  num.cores = 1L,
  tasks = 0,
  verbose = TRUE,
  ...
)

## S4 method for signature 'pDMP'
getGRegionsStat(
  GR,
  win.size = 350,
  step.size = 350,
  grfeatures = NULL,
  stat = c("sum", "mean", "gmean", "median", "density", "count", "denCount"),
  absolute = FALSE,
  select.strand = NULL,
  column = 1L,
  prob = FALSE,
  entropy = FALSE,
  maxgap = -1L,
  minoverlap = 0L,
  scaling = 1000L,
  logbase = 2,
  missings = 0,
  type = c("within", "any", "start", "end", "equal"),
  ignore.strand = FALSE,
  naming = FALSE,
  col.names = NULL,
  output = c("hits", "all"),
  num.cores = 1L,
  tasks = 0,
  verbose = TRUE,
  ...
)

## S4 method for signature 'GRangesList'
getGRegionsStat(
  GR,
  win.size = 350,
  step.size = 350,
  grfeatures = NULL,
  stat = c("sum", "mean", "gmean", "median", "density", "count", "denCount"),
  absolute = FALSE,
  select.strand = NULL,
  column = 1L,
  prob = FALSE,
  entropy = FALSE,
  maxgap = -1L,
  minoverlap = 0L,
  scaling = 1000L,
  logbase = 2,
  missings = 0,
  type = c("within", "any", "start", "end", "equal"),
  ignore.strand = FALSE,
  naming = FALSE,
  col.names = NULL,
  output = c("hits", "all"),
  num.cores = 1L,
  tasks = 0,
  verbose = TRUE,
  ...
)

Arguments

GR	A GRange object or a list of GRanges object with the variable of interest in the GRanges metacolumn.
win.size	An integer for the size of the windows/regions size of the intervals of genomics regions.
step.size	Interval at which the regions/windows must be defined
grfeatures	A GRanges object corresponding to an annotated genomic feature. For example, gene region, transposable elements, exons, intergenic region, etc. If provided, then parameters 'win.size' and step.size are ignored and the statistics are estimated for 'grfeatures'.
stat	Statistic used to estimate the summarized value of the variable of interest in each interval/window. Posible options are: 'mean': The mean of values inside each region. 'gmean': The geometric mean of values inside each region. 'median': The median of values inside each region. 'density': The density of values inside each region. That is, the sum of values found in each region divided by the width of the region. 'count': Compute the number/count of positions with values greater than zero inside each regions. 'denCount': The number of sites with value > 0 inside each region divided by the width of the region. 'sum': The sum of values inside each region.
absolute	Optional. Logic (default: FALSE). Whether to use the absolute values of the variable provided. For example, the difference of methylation levels could take negative values (TV) and we would be interested on the sum of abs(TV), which is sum of the total variation distance.
select.strand	Optional. If provided,'+' or '-', then the summarized statistic is computed only for the specified DNA chain.
column	Integer number denoting the column where the variable of interest is located in the metacolumn of the GRanges object.
prob	Logic. If TRUE and the variable of interest has values between zero and 1, then the summarized statistic is comuputed using Fisher's transformation.
entropy	Logic. Whether to compute the entropy at each site from the specified regions. All the values from the selected column must belong to the interval [0, 1]. Next, the requested statistics for the entropy values at each site inside the regions is computed.
maxgap, minoverlap, type	See ?findOverlaps in the IRanges package for a description of these arguments.
scaling	integer (default 1). Scaling factor to be used when stat = 'density'. For example, if scaling = 1000, then density * scaling denotes the sum of values in 1000 bp.
logbase	A positive number: the base with respect to which logarithms are computed when parameter 'entropy = TRUE' (default: logbase = 2).
missings	Whether to write '0' or 'NA' on regions where there is not data to compute the statistic.
ignore.strand	When set to TRUE, the strand information is ignored in the overlap calculations.
naming	Logical value. If TRUE, the rows GRanges object will be given the names(GR). Default is FALSE.
col.names	Optional. An integer denoting the column where the names/gene-id of each region is provided. If naming = TRUE and the names/gene-id of the regions are given in specific column from the object grfeatures, then col.names can be specified. Region's names can be also given as names in object grfeatures, i.e., they can be taken calling names(grfeatures). In this last case col.names is not needed.
output	A string. Setting output = 'all' will return all the regions given in 'grfeatures'. Default is output = 'hits'.
verbose	Logical. Default is TRUE. If TRUE, then the progress of the computational tasks is given.
num.cores, tasks	Paramaters for parallele computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
maxgap, minoverlap, type, select, ignore.strand	Used to find overlapped regions. See findOverlaps-methods in the IRanges package for a description of these arguments.

Details

This function split a Grange object into intervals genomic regions (GR) of fixed size (as given in function 'tileMethylCounts2' R package methylKit, with small changes). A summarized statistic (mean, median, geometric mean or sum) is calculated for the specified variable values from each region. Notice that if win.size == step.size, then non-overlapping windows are obtained.

Value

An object of the same class of GR with the new genomic regions and their corresponding summarized statistic.

Author(s)

Robersy Sanchez (https://github.com/genomaths).

See Also

getGRegionsStat2.

Examples

library(GenomicRanges)
gr <- GRanges(seqnames = Rle( c('chr1', 'chr2', 'chr3', 'chr4'),
            c(5, 5, 5, 5)),
            ranges = IRanges(start = 1:20, end = 1:20),
            strand = rep(c('+', '-'), 10),
            GC = seq(1, 0, length = 20))
grs <- getGRegionsStat(gr, win.size = 4, step.size = 4)
grs

## Selecting the positive strand
grs <- getGRegionsStat(gr, win.size = 4, step.size = 4, select.strand = '+')
grs

## Selecting the negative strand
grs <- getGRegionsStat(gr, win.size = 4, step.size = 4, select.strand = '-')
grs

## Operating over a list of GRanges objects
gr2 <- GRanges(seqnames = Rle( c('chr1', 'chr2', 'chr3', 'chr4'),
                            c(5, 5, 5, 5)),
                ranges = IRanges(start = 1:20, end = 1:20),
                strand = rep(c('+', '-'), 10),
                GC = runif(20))

grs <- getGRegionsStat(list(gr1 = gr, gr2 = gr2), win.size = 4, step.size=4)

## Compute the density of entropy inside each region
gr$GC <- runif(20) 
getGRegionsStat(gr, win.size = 4, step.size = 4, entropy = TRUE, 
                stat = "density")
                

genomaths/MethylIT.utils documentation built on July 4, 2023, 12:05 a.m.