coverageOverRanges: Coverage function for BSFDataSet objects

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

Coverage function for BSFDataSet objects

Description

The crosslink coverage is computed for all ranges in the the given BSFDataSet object (see BSFDataSet for details). Depending on the returnOptions the resulting coverage information is summarized, suitable for diverse computation and plotting tasks. The coverage can only be compute for objects with identical ranges.

Usage

coverageOverRanges(
  object,
  returnOptions = c("merge_ranges_keep_positions", "merge_replicates_per_condition",
    "merge_all_replicates", "merge_positions_keep_replicates"),
  method = "sum",
  allowNA = FALSE,
  quiet = TRUE
)

Arguments

object	a BSFDataSet object
returnOptions	one of merge_ranges_keep_positions, merge_replicates_per_condition, merge_all_replicates, merge_positions_keep_replicates
method	sum/ mean, select how replicates/ ranges should be summarized
allowNA	TRUE/ FALSE, allow NA values in the output if input ranges are of different width
quiet	logical, whether to print messages

Details

If returnOptions is set to merge_ranges_keep_positions: Returns a matrix with ncol being the nucleotides of the ranges (equal to the width of the input ranges) and nrow being the number of replicates in the meta information.

If returnOptions is set to merge_replicates_per_condition: Returns a list of matrices. Each list corresponds to one condition set in the meta information. The matrix in each entry has ncols equal to the ranges width and nrow equal to the number of ranges. Counts per ranges and position are summed.

If returnOptions is set to merge_all_replicates: Returns a matrix with ncols equal to the range width and nrow equal to the number of ranges. Counts per range and position are summed.

If returnOptions is set to merge_positions_keep_replicates: Returns a GRanges object where the counts are summed for each replicate and added to the original granges object.

Value

an object of class specified in returnOptions

Examples

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

rng = coverageOverRanges(bds, returnOptions = "merge_ranges_keep_positions")
rng = coverageOverRanges(bds, returnOptions = "merge_replicates_per_condition")
rng = coverageOverRanges(bds, returnOptions = "merge_all_replicates")
rng = coverageOverRanges(bds, returnOptions = "merge_positions_keep_replicates")

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